HEADER HYDROLASE 27-OCT-00 1G4I TITLE CRYSTAL STRUCTURE OF THE BOVINE PANCREATIC PHOSPHOLIPASE A2 AT 0.97A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS LIPID DEGRADATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.A.STEINER,H.J.ROZEBOOM,A.DE VRIES,K.H.KALK,G.N.MURSHUDOV, AUTHOR 2 K.S.WILSON,B.W.DIJKSTRA REVDAT 4 13-JUL-11 1G4I 1 VERSN REVDAT 3 03-NOV-09 1G4I 1 HETATM REVDAT 2 24-FEB-09 1G4I 1 VERSN REVDAT 1 04-APR-01 1G4I 0 JRNL AUTH R.A.STEINER,H.J.ROZEBOOM,A.DE VRIES,K.H.KALK,G.N.MURSHUDOV, JRNL AUTH 2 K.S.WILSON,B.W.DIJKSTRA JRNL TITL X-RAY STRUCTURE OF BOVINE PANCREATIC PHOSPHOLIPASE A2 AT JRNL TITL 2 ATOMIC RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 516 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11264580 JRNL DOI 10.1107/S0907444901002530 REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.094 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) : 66635 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 957 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 247 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.021 REMARK 3 ANGLE DISTANCES (A) : 0.046 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.013 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.111 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.118 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.099 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.076 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1G4I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-00. REMARK 100 THE RCSB ID CODE IS RCSB012222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.670 REMARK 200 MONOCHROMATOR : 2 CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66635 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.040 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.28 REMARK 200 R MERGE FOR SHELL (I) : 0.17200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.890 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1UNE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, CALCIUM CHLORIDE, TRIS BUFFER, PH REMARK 280 7.6, SMALL TUBES, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 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 -1.000000 0.000000 0.000000 23.26600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.81200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.77850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 18.81200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.26600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.77850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 24 CG OD1 ND2 REMARK 480 LYS A 108 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE A 106 CB - CG - CD1 ANGL. DEV. = 5.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 339 DISTANCE = 5.07 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 124 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 28 O REMARK 620 2 GLY A 30 O 92.7 REMARK 620 3 GLY A 32 O 100.9 78.6 REMARK 620 4 ASP A 49 OD1 100.9 145.6 128.4 REMARK 620 5 ASP A 49 OD2 94.2 158.5 80.1 52.1 REMARK 620 6 HOH A 136 O 77.8 76.3 154.8 75.9 125.1 REMARK 620 7 HOH A 143 O 177.5 86.5 81.2 78.6 87.4 99.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 124 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 128 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 129 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 126 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 130 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UNE RELATED DB: PDB REMARK 900 1.5A - ENGINEERED REMARK 900 RELATED ID: 1BP2 RELATED DB: PDB REMARK 900 1.7A - WILD-TYPE DBREF 1G4I A 1 123 UNP P00593 PA21B_BOVIN 23 145 SEQADV 1G4I ASN A 122 UNP P00593 LYS 144 CONFLICT SEQRES 1 A 123 ALA LEU TRP GLN PHE ASN GLY MET ILE LYS CYS LYS ILE SEQRES 2 A 123 PRO SER SER GLU PRO LEU LEU ASP PHE ASN ASN TYR GLY SEQRES 3 A 123 CYS TYR CYS GLY LEU GLY GLY SER GLY THR PRO VAL ASP SEQRES 4 A 123 ASP LEU ASP ARG CYS CYS GLN THR HIS ASP ASN CYS TYR SEQRES 5 A 123 LYS GLN ALA LYS LYS LEU ASP SER CYS LYS VAL LEU VAL SEQRES 6 A 123 ASP ASN PRO TYR THR ASN ASN TYR SER TYR SER CYS SER SEQRES 7 A 123 ASN ASN GLU ILE THR CYS SER SER GLU ASN ASN ALA CYS SEQRES 8 A 123 GLU ALA PHE ILE CYS ASN CYS ASP ARG ASN ALA ALA ILE SEQRES 9 A 123 CYS PHE SER LYS VAL PRO TYR ASN LYS GLU HIS LYS ASN SEQRES 10 A 123 LEU ASP LYS LYS ASN CYS HET CA A 124 1 HET CL A 125 1 HET MRD A 127 8 HET MRD A 128 8 HET MRD A 129 8 HET MPD A 126 8 HET MPD A 130 8 HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 CA CA 2+ FORMUL 3 CL CL 1- FORMUL 4 MRD 3(C6 H14 O2) FORMUL 7 MPD 2(C6 H14 O2) FORMUL 9 HOH *247(H2 O) HELIX 1 1 ALA A 1 ILE A 13 1 13 HELIX 2 2 GLU A 17 PHE A 22 1 6 HELIX 3 3 ASP A 39 LEU A 58 1 20 HELIX 4 4 LEU A 58 LEU A 64 1 7 HELIX 5 5 ASN A 67 ASN A 71 5 5 HELIX 6 6 ASN A 89 LYS A 108 1 20 HELIX 7 7 ASN A 112 HIS A 115 5 4 HELIX 8 8 ASP A 119 CYS A 123 5 5 SHEET 1 A 2 TYR A 75 SER A 78 0 SHEET 2 A 2 GLU A 81 CYS A 84 -1 O GLU A 81 N SER A 78 SSBOND 1 CYS A 11 CYS A 77 1555 1555 2.03 SSBOND 2 CYS A 27 CYS A 123 1555 1555 2.02 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.03 SSBOND 4 CYS A 44 CYS A 105 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.04 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.04 LINK O TYR A 28 CA CA A 124 1555 1555 2.35 LINK O AGLY A 30 CA CA A 124 1555 1555 2.32 LINK O BGLY A 30 CA CA A 124 1555 1555 2.48 LINK O AGLY A 32 CA CA A 124 1555 1555 2.32 LINK O BGLY A 32 CA CA A 124 1555 1555 2.36 LINK OD1 ASP A 49 CA CA A 124 1555 1555 2.47 LINK OD2 ASP A 49 CA CA A 124 1555 1555 2.50 LINK CA CA A 124 O HOH A 136 1555 1555 2.41 LINK CA CA A 124 O HOH A 143 1555 1555 2.36 SITE 1 AC1 6 TYR A 28 GLY A 30 GLY A 32 ASP A 49 SITE 2 AC1 6 HOH A 136 HOH A 143 SITE 1 AC2 4 LYS A 12 ILE A 82 ARG A 100 HOH A 356 SITE 1 AC3 7 ASN A 6 PHE A 22 ASN A 23 GLY A 30 SITE 2 AC3 7 MPD A 126 MRD A 128 HOH A 136 SITE 1 AC4 12 LEU A 2 PHE A 5 ASN A 6 PRO A 18 SITE 2 AC4 12 LEU A 19 PHE A 22 ASN A 23 CYS A 29 SITE 3 AC4 12 GLY A 30 PHE A 106 MPD A 126 MRD A 127 SITE 1 AC5 5 SER A 15 SER A 16 ASP A 21 GLN A 54 SITE 2 AC5 5 HOH A 162 SITE 1 AC6 7 GLY A 30 LEU A 31 MRD A 127 MRD A 128 SITE 2 AC6 7 HOH A 136 HOH A 169 HOH A 240 SITE 1 AC7 12 LYS A 10 GLU A 17 LEU A 19 LEU A 20 SITE 2 AC7 12 CYS A 105 VAL A 109 HOH A 141 HOH A 149 SITE 3 AC7 12 HOH A 189 HOH A 315 HOH A 357 HOH A 358 CRYST1 46.532 63.557 37.624 90.00 90.00 90.00 P 21 21 21 4 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 0.021490 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026580 0.00000 MASTER 267 0 7 8 2 0 15 6 0 0 0 10 END