HEADER HYDROLASE 04-MAY-92 1BBC TITLE STRUCTURE OF RECOMBINANT HUMAN RHEUMATOID ARTHRITIC SYNOVIAL FLUID TITLE 2 PHOSPHOLIPASE A2 AT 2.2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CARBOXYLIC ESTER HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-P.WERY,R.W.SCHEVITZ,D.K.CLAWSON,J.L.BOBBITT,E.R.DOW,G.GAMBOA, AUTHOR 2 T.GOODSONJUNIOR,R.B.HERMANN,R.M.KRAMER,D.B.MCCLURE,E.D.MIHELICH, AUTHOR 3 J.E.PUTNAM,J.D.SHARP,D.H.STARK,C.TEATER,M.W.WARRICK,N.D.JONES REVDAT 6 14-AUG-19 1BBC 1 REMARK REVDAT 5 17-JUL-19 1BBC 1 REMARK REVDAT 4 29-FEB-12 1BBC 1 JRNL VERSN REVDAT 3 24-FEB-09 1BBC 1 VERSN REVDAT 2 01-APR-03 1BBC 1 JRNL REVDAT 1 31-OCT-93 1BBC 0 JRNL AUTH J.P.WERY,R.W.SCHEVITZ,D.K.CLAWSON,J.L.BOBBITT,E.R.DOW, JRNL AUTH 2 G.GAMBOA,T.GOODSON JR.,R.B.HERMANN,R.M.KRAMER,D.B.MCCLURE, JRNL AUTH 3 E.D.MIHELICH,J.E.PUTNAM,J.D.SHARP,D.H.STARK,C.TEATER, JRNL AUTH 4 M.W.WARRICK,N.D.JONES JRNL TITL STRUCTURE OF RECOMBINANT HUMAN RHEUMATOID ARTHRITIC SYNOVIAL JRNL TITL 2 FLUID PHOSPHOLIPASE A2 AT 2.2 A RESOLUTION. JRNL REF NATURE V. 352 79 1991 JRNL REFN ISSN 0028-0836 JRNL PMID 2062381 JRNL DOI 10.1038/352079A0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.M.KRAMER,C.HESSION,B.JOHANSEN,G.HAYES,P.MCGRAY,E.P.CHOW, REMARK 1 AUTH 2 R.TIZARD,R.B.PEPINSKY REMARK 1 TITL STRUCTURE AND PROPERTIES OF A HUMAN NON-PANCREATIC REMARK 1 TITL 2 PHOSPHOLIPASE A2 REMARK 1 REF J.BIOL.CHEM. V. 264 5768 1989 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4114 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL 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) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 966 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.636 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.555 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.657 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.835 ; 3.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171555. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 27.28000 REMARK 290 SMTRY3 2 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLN A 88 OG SER A 93 2.07 REMARK 500 O ASN A 122 N HIS A 124 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 43 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 43 NE - CZ - NH2 ANGL. DEV. = 6.0 DEGREES REMARK 500 CYS A 44 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 49 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 58 CD - NE - CZ ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 81 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 GLN A 88 CB - CG - CD ANGL. DEV. = 16.6 DEGREES REMARK 500 ASP A 89 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 108 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 CYS A 125 CB - CA - C ANGL. DEV. = 10.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 16 95.65 -56.06 REMARK 500 ASP A 39 -164.99 -160.74 REMARK 500 LEU A 55 34.40 -68.93 REMARK 500 LYS A 57 -178.36 166.17 REMARK 500 CYS A 61 74.40 103.32 REMARK 500 THR A 68 -95.76 -128.43 REMARK 500 SER A 78 -159.35 177.39 REMARK 500 SER A 80 10.58 -141.01 REMARK 500 ARG A 81 -125.94 83.72 REMARK 500 ALA A 85 -142.50 -77.80 REMARK 500 LYS A 86 -130.18 -0.38 REMARK 500 GLN A 88 -45.11 -158.17 REMARK 500 ASP A 89 135.69 -11.62 REMARK 500 ASN A 109 40.55 -94.81 REMARK 500 LYS A 123 -23.21 -29.73 REMARK 500 HIS A 124 67.37 -165.51 REMARK 500 PRO A 130 106.93 -56.34 REMARK 500 ARG A 131 134.99 -39.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BBC A 1 132 UNP P14555 PA2GA_HUMAN 21 144 SEQRES 1 A 124 ASN LEU VAL ASN PHE HIS ARG MET ILE LYS LEU THR THR SEQRES 2 A 124 GLY LYS GLU ALA ALA LEU SER TYR GLY PHE TYR GLY CYS SEQRES 3 A 124 HIS CYS GLY VAL GLY GLY ARG GLY SER PRO LYS ASP ALA SEQRES 4 A 124 THR ASP ARG CYS CYS VAL THR HIS ASP CYS CYS TYR LYS SEQRES 5 A 124 ARG LEU GLU LYS ARG GLY CYS GLY THR LYS PHE LEU SER SEQRES 6 A 124 TYR LYS PHE SER ASN SER GLY SER ARG ILE THR CYS ALA SEQRES 7 A 124 LYS GLN ASP SER CYS ARG SER GLN LEU CYS GLU CYS ASP SEQRES 8 A 124 LYS ALA ALA ALA THR CYS PHE ALA ARG ASN LYS THR THR SEQRES 9 A 124 TYR ASN LYS LYS TYR GLN TYR TYR SER ASN LYS HIS CYS SEQRES 10 A 124 ARG GLY SER THR PRO ARG CYS FORMUL 2 HOH *87(H2 O) HELIX 1 H1 ASN A 1 THR A 13 1 13 HELIX 2 H2 ALA A 17 SER A 20 1 4 HELIX 3 H3 ALA A 40 ARG A 54 1 15 HELIX 4 H4 SER A 90 ARG A 108 1 19 SHEET 1 SH1 2 LYS A 74 SER A 78 0 SHEET 2 SH1 2 ARG A 81 ALA A 85 -1 SSBOND 1 CYS A 27 CYS A 125 1555 1555 2.09 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.10 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.15 SSBOND 4 CYS A 50 CYS A 132 1555 1555 2.11 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.18 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.10 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.10 CRYST1 31.610 54.560 31.320 90.00 97.20 90.00 P 1 21 1 2 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 0.031636 0.000000 0.003996 0.00000 SCALE2 0.000000 0.018328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032182 0.00000