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PDB Pipeline

PDB Pipeline. October 19, 2006. History of the PDB. 1970s Community discussions about how to establish an archive of protein structures Cold Spring Harbor meeting in protein crystallography PDB established at Brookhaven (October 1971; 7 structures) 1980s

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PDB Pipeline

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  1. PDB Pipeline October 19, 2006

  2. History of the PDB 1970s • Community discussions about how to establish an archive of protein structures • Cold Spring Harbor meeting in protein crystallography • PDB established at Brookhaven (October 1971; 7 structures) 1980s • Number of structures increases as technology improves • Community discussions about requiring depositions • IUCr guidelines established • Number of structures deposited increases 1990s • Structural genomics begins • PDB moves to RCSB 2000s • wwPDB formed

  3. Number of released entries Year

  4. Structure Determination Pipeline(X-ray) Hypothesis Driven Target Selection Data Collection Structure Determination Publication Crystallomics Data Deposition Data Release Isolation, Expression, Purification,Crystallization

  5. The Data Pipeline

  6. Content of Data FilesPDB Archive • Macromolecular coordinates (~31,000) • Description of experiment • Description of chemical content (protein, ligands, solvent) • Description of structural features (secondary structure) >2000 data items defined 300-1200 populated

  7. HEADER HYDROLASE 20-AUG-99 1CTW TITLE T4 LYSOZYME MUTANT I78A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE T4; SOURCE 3 ORGANISM_COMMON: VIRUS; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_VECTOR: PHS1403 KEYWDS HYDROLASE (O-GLYCOSYL), T4 LYSOZYME, CAVITY MUTANT, PROTEIN KEYWDS 2 ENGINEERING, PROTEIN FOLDING EXPDTA X-RAY DIFFRACTION AUTHOR N.C.GASSNER,W.A.BAASE,J.D.LINDSTROM,J.LU,B.W.MATTHEWS REVDAT 3 30-JUN-00 1CTW 1 REMARK SOURCE REVDAT 2 08-DEC-99 1CTW 1 COMPND REMARK SEQRES DBREF REVDAT 1 10-NOV-99 1CTW 0

  8. JRNL AUTH N.C.GASSNER,W.A.BAASE,J.D.LINDSTROM,J.LU, JRNL AUTH 2 F.W.DAHLQUIST,B.W.MATTHEWS JRNL TITL METHIONINE AND ALANINE SUBSTITUTIONS SHOW THAT THE JRNL TITL 2 FORMATION OF WILD-TYPE-LIKE STRUCTURE IN THE JRNL TITL 3 CARBOXY-TERMINAL DOMAIN OF T4 LYSOZYME IS A JRNL TITL 4 RATE-LIMITING STEP IN FOLDING JRNL REF BIOCHEMISTRY V. 38 14451 1999 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.XU,W.A.BAASE,E.BALDWIN,B.W.MATTHEWS REMARK 1 TITL THE RESPONSE OF T4 LYSOZYME TO LARGE-TO-SMALL REMARK 1 TITL 2 SUBSTITUTIONS WITHIN THE CORE AND ITS RELATION TO REMARK 1 TITL 3 THE HYDROPHOBIC EFFECT REMARK 1 REF PROTEIN SCI. V. 7 158 1998 REMARK 1 REFN ASTM PRCIEI US ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.H.WEAVER,B.W.MATTHEWS REMARK 1 TITL STRUCTURE OF BACTERIOPHAGE T4 LYSOZYME REFINED AT REMARK 1 TITL 2 1.7 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 193 189 1987 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836

  9. REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.0 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11183 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD :NULL REMARK 3 FREE R VALUE TEST SET SELECTION :NULL REMARK 3 R VALUE (WORKING + TEST SET) :0.172 REMARK 3 R VALUE (WORKING SET) :0.172 REMARK 3 FREE R VALUE :NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) :NULL REMARK 3 FREE R VALUE TEST SET COUNT :NULL

  10. REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1720 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11183 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1289 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.019 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.600 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL

  11. REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CTW COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 6 REMARK 6 RESIDUES 163 AND 164 WERE MISSING IN THE ELECTRON DENSITY. REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-1999. REMARK 100 THE RCSB ID CODE IS RCSB009539.

  12. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-1998 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : R-AXIS

  13. REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11183 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200

  14. REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: TNT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA2PO4, NACL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1

  15. REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,2/3+Z REMARK 290 3555 -X+Y,-X,1/3+Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,1/3-Z REMARK 290 6555 -X,-X+Y,2/3-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290

  16. REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.14000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.57000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.57000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.14000 REMARK 290 REMARK 290 REMARK: NULL

  17. REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465

  18. REMARK 465 M RES C SSSEQI REMARK 465 ASN A 163 REMARK 465 LEU A 164 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 0 HOH 297 DISTANCE = 6.85 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CU0 RELATED DB: PDB REMARK 900 T4 LYSOZYME MUTANT I78M REMARK 900 RELATED ID: 1CU2 RELATED DB: PDB REMARK 900 T4 LYSOZYME MUTANT L84M REMARK 900 RELATED ID: 1CU3 RELATED DB: PDB REMARK 900 T4 LYSOZYME MUTANT V87M REMARK 900 RELATED ID: 1CU6 RELATED DB: PDB REMARK 900 T4 LYSOZYME MUTANT L91A

  19. DBREF 1CTW A 1 164 SWS P00720 LYCV_BPT4 1 164 SEQADV 1CTW THR A 54 SWS P00720 CYS 54 ENGINEERED SEQADV 1CTW ALA A 97 SWS P00720 CYS 97 ENGINEERED SEQADV 1CTW ALA A 78 SWS P00720 ILE 78 ENGINEERED SEQRES 1 A 164 MET ASN ILE PHE GLU MET LEU ARG ILE ASP GLU GLY LEU SEQRES 2 A 164 ARG LEU LYS ILE TYR LYS ASP THR GLU GLY TYR TYR THR SEQRES 3 A 164 ILE GLY ILE GLY HIS LEU LEU THR LYS SER PRO SER LEU SEQRES 4 A 164 ASN ALA ALA LYS SER GLU LEU ASP LYS ALA ILE GLY ARG SEQRES 5 A 164 ASN THR ASN GLY VAL ILE THR LYS ASP GLU ALA GLU LYS SEQRES 6 A 164 LEU PHE ASN GLN ASP VAL ASP ALA ALA VAL ARG GLY ALA SEQRES 7 A 164 LEU ARG ASN ALA LYS LEU LYS PRO VAL TYR ASP SER LEU SEQRES 8 A 164 ASP ALA VAL ARG ARG ALA ALA LEU ILE ASN MET VAL PHE SEQRES 9 A 164 GLN MET GLY GLU THR GLY VAL ALA GLY PHE THR ASN SER SEQRES 10 A 164 LEU ARG MET LEU GLN GLN LYS ARG TRP ASP GLU ALA ALA SEQRES 11 A 164 VAL ASN LEU ALA LYS SER ARG TRP TYR ASN GLN THR PRO SEQRES 12 A 164 ASN ARG ALA LYS ARG VAL ILE THR THR PHE ARG THR GLY SEQRES 13 A 164 THR TRP ASP ALA TYR LYS ASN LEU HET CL 178 1 HET HED 170 8 HETNAM CL CHLORIDE ION HETNAM HED 2-HYDROXYETHYL DISULFIDE

  20. FORMUL 2 CL CL1 1- FORMUL 3 HED C4 H10 O2 S2 FORMUL 4 HOH *98(H2 O1) HELIX 1 1 ASN A 2 GLY A 12 1 11 HELIX 2 2 SER A 38 GLY A 51 1 14 HELIX 3 3 THR A 59 ASN A 81 1 23 HELIX 4 4 LYS A 83 LEU A 91 1 9 HELIX 5 5 ASP A 92 GLY A 107 1 16 HELIX 6 6 MET A 106 GLY A 113 1 8 HELIX 7 7 PHE A 114 GLN A 123 1 10 HELIX 8 8 ARG A 125 LYS A 135 1 11 HELIX 9 9 SER A 136 THR A 142 1 7 HELIX 10 10 THR A 142 GLY A 156 1 15 HELIX 11 11 TRP A 158 LYS A 162 5 5 SHEET 1 A 3 ARG A 14 LYS A 19 0 SHEET 2 A 3 TYR A 25 GLY A 28 -1 N THR A 26 O TYR A 18 SHEET 3 A 3 HIS A 31 THR A 34 -1 N HIS A 31 O ILE A 27 CRYST1 61.130 61.130 97.710 90.00 90.00 120.00 P 32 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016359 0.009445 0.000000 0.00000 SCALE2 0.000000 0.018889 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010234 0.00000

  21. The Data Processing Pipeline

  22. Depositor Validation MAXIT Data ADIT AutoDep Input Tool Database Loader Reports Final Files Metadata Dictionaries Data Views System for Data Collection and Archiving

  23. Data Processing System Features Different dictionaries without software changes Simple customization of both functionality and content Automatically scales with changes in content Can be distributed to multiple deposition sites Reference data and standard nomenclature (ERFs)

  24. Sequence-Structure checks • Run BLAST for every structure • Review annotations in PDB files and sequence files • Check for SEQRES-atom site discrepancies • Resolve discrepancies with author

  25. Ligand checks • Chemical name • Chemical structure • If new ligand define chemistry including stereochemistry • Bond order • Nomenclature • Chirality

  26. Structure Checks • Covalent geometry • Intermolecular close contacts • Distant waters and ligands • Atom nomenclatures • Chirality • Missing atoms • PROCHECK, NUCHECK, Molprobity checks

  27. “fair” “good”

  28. Experimental Data • SFCheck • Review R factor, resolution, real space R’s for each residue

  29. Validation letter Oct. 15, 16:19:01 2002 Thank you for using RCSB. The following geometrical and stereochemical features have been calculated for your structure: CLOSE CONTACTS -------------- ==> Close contacts in same asymmetric unit. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Close contacts based on crystal symmetry. Distances smaller than 2.2 Angstroms are considered as close contacts. none

  30. BOND DISTANCES AND ANGLES ------------------------- ==> Bond and angle checks are performed by first computing the average rms error for all bonds and angles relative to standard values for nucleotide units [L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases, J.Am.Chem.Soc. 1996, 118, 509-518; A. Gelbin et al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J.Am.Chem.Soc. 1996, 118, 519-529] and amino acid units [R.A. Engh and R. Huber, Accurate Bond and Angle Parameters for X-ray protein structure refinement, Acta Crystallogr. 1991, A47, 392-400]. Any bond or angle which deviates from the dictionary values by more than four times this computed rms error is identified as an outlier.

  31. *** Covalent Bond Lengths: The RMS deviation for covalent bonds relative to the standard dictionary is 0.023 Angstroms All covalent bonds lie within a 6.0*RMSD range about the standard dictionary values. *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 2.7 degrees. All covalent bond angles lie within a 6.0*RMSD range about the standard dictionary values.

  32. TORSION ANGLES -------------- The torsion angle distributions have been checked. Refer to the Procheck and/or Nucheck results on the RCSB Validation Report page. SOLVENT ------- The following solvent molecules are further than 3.5 Angstroms away from macromolecule atoms in the asymmetric unit that are available for hydrogen bonding. Solvent molecules in extended hydration shells separated by 3.5 Angstroms or less are not listed. HETATM 1356 O HOH 247 46.616 26.527 14.884 1.00 57.43 O HETATM 1368 O HOH 272 17.563 13.735 -6.087 1.00 66.94 O HETATM 1379 O HOH 296 42.200 -6.696 5.941 1.00 65.35 O HETATM 1380 O HOH 297 41.523 -9.207 2.671 1.00 60.36 O

  33. The coordinates for water molecules which could be translated back into the asymmetric unit are listed. If you do not indicate otherwise we will replace the solvent coordinates in the entry with the ones below: HETATM 1356 O HOH 247 30.230 0.694 -14.884 1.00 57.43 O HETATM 1368 O HOH 272 33.678 30.863 26.483 1.00 66.94 O HETATM 1379 O HOH 296 42.200 6.696 26.629 1.00 65.35 O HETATM 1380 O HOH 297 41.523 9.207 29.899 1.00 60.36 O MISSING RESIDUES ---------------- ==> The following residues are missing: (Note: The SEQ number starts from 1 for each chain according to SEQRES sequence record.) RES MOD#C SEQ ASN( A 163 ) LEU( A 164 )

  34. PDB Chain_ID: A 1 15 SEQRES: MET ASN ILE PHE GLU MET LEU ARG ILE ASP GLU GLY LEU ARG LEU COORDS: MET ASN ILE PHE GLU MET LEU ARG ILE ASP GLU GLY LEU ARG LEU 1 15 16 30 SEQRES: LYS ILE TYR LYS ASP THR GLU GLY TYR TYR THR ILE GLY ILE GLY COORDS: LYS ILE TYR LYS ASP THR GLU GLY TYR TYR THR ILE GLY ILE GLY 16 30 31 45 SEQRES: HIS LEU LEU THR LYS SER PRO SER LEU ASN ALA ALA LYS SER GLU COORDS: HIS LEU LEU THR LYS SER PRO SER LEU ASN ALA ALA LYS SER GLU 31 45 46 60 SEQRES: LEU ASP LYS ALA ILE GLY ARG ASN THR ASN GLY VAL ILE THR LYS COORDS: LEU ASP LYS ALA ILE GLY ARG ASN THR ASN GLY VAL ILE THR LYS 46 60

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