HEADER HYDROLASE 31-MAY-02 1LWB TITLE CRYSTAL STRUCTURE OF PROKARYOTIC PHOSPHOLIPASE A2 AT ATOMIC RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SECRETED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOLIPASE A2; COMPND 5 EC: 3.1.1.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VIOLACEORUBER; SOURCE 3 ORGANISM_TAXID: 1935; SOURCE 4 EXPRESSION_SYSTEM: STREPTOMYCES LIVIDANS TK24; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 457428; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: TK24; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PIJ680 KEYWDS PHOSPHOLIPASE A2, ATOMIC RESOLUTION, INTERNAL MOTION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MATOBA,M.SUGIYAMA REVDAT 3 11-OCT-17 1LWB 1 REMARK REVDAT 2 24-FEB-09 1LWB 1 VERSN REVDAT 1 10-JUN-03 1LWB 0 JRNL AUTH Y.MATOBA,M.SUGIYAMA JRNL TITL ATOMIC RESOLUTION STRUCTURE OF PROKARYOTIC PHOSPHOLIPASE A2: JRNL TITL 2 ANALYSIS OF INTERNAL MOTION AND IMPLICATION FOR A CATALYTIC JRNL TITL 3 MECHANISM. JRNL REF PROTEINS: V. 51 453 2003 JRNL REF 2 STRUCT.,FUNCT.,GENET. JRNL REFN ISSN 0887-3585 JRNL PMID 12696056 JRNL DOI 10.1002/PROT.10360 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.MATOBA,Y.KATSUBE,M.SUGIYAMA REMARK 1 TITL THE CRYSTAL STRUCTURE OF PROKARYOTIC PHOSPHOLIPASE A2 REMARK 1 REF J.BIOL.CHEM. V. 277 20059 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M200263200 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.SUGIYAMA,K.OHTANI,M.IZUHARA,T.KOIKE,K.SUZUKI,S.IMAMURA, REMARK 1 AUTH 2 H.MISAKI REMARK 1 TITL A NOVEL PROKARYOTIC PHOSPHOLIPASE A2. CHARACTERIZATON, GENE REMARK 1 TITL 2 CLONING AND SOLUTION STRUCTURE REMARK 1 REF J.BIOL.CHEM. V. 277 20051 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M200264200 REMARK 2 REMARK 2 RESOLUTION. 1.05 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.103 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.097 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3423 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 37649 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.090 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.087 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.128 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2934 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 31531 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1120.7 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 844.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 34 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10812 REMARK 3 NUMBER OF RESTRAINTS : 13414 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 ANGLE DISTANCES (A) : 0.035 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.023 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.104 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.128 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.035 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.010 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.044 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.132 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: ANISOTROPIC TEMPERATURE FACTOR WAS REMARK 3 INTRODUCED. REMARK 4 REMARK 4 1LWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1997 REMARK 200 TEMPERATURE (KELVIN) : 297 REMARK 200 PH : 6 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) : 0.71073 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45532 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.923 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 67.5 REMARK 200 DATA REDUNDANCY : 2.650 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 22.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.640 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1FAZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 17.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, LITHIUM SULFATE, SODIUM REMARK 280 CACODYLATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K, PH 6 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 28.74750 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 300 REMARK: THIS ENZYME IS A MONOMERIC PROTEIN IN SOLUTION. 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: 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 ASP A 50 CB - CG - OD1 ANGL. DEV. = -7.3 DEGREES REMARK 500 ASP A 50 CB - CG - OD2 ANGL. DEV. = 10.3 DEGREES REMARK 500 TYR A 68 CB - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TYR A 68 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 85 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 TYR A 99 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 TYR A 99 CG - CD2 - CE2 ANGL. DEV. = 5.0 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 LEU A 44 -138.43 56.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FAZ RELATED DB: PDB REMARK 900 1FAZ CONTAINS CRYSTAL STRUCTURE OF CALCIUM-FREE FORM AT 1.4 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 1KP4 RELATED DB: PDB REMARK 900 1KP4 CONTAINS CRYSTAL STRUCTURE OF CALCIUM-BOUND FORM AT 1.6 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 1IT4 RELATED DB: PDB REMARK 900 1IT4 CONTAINS SOLUTION STRUCTURE OF CALCIUM-BOUND FORM REMARK 900 RELATED ID: 1IT5 RELATED DB: PDB REMARK 900 1IT5 CONTAINS SOLUTION STRUCTURE OF CALCIUM-FREE FORM DBREF 1LWB A 1 122 UNP Q9Z4W2 Q9Z4W2_STRCO 30 151 SEQRES 1 A 122 ALA PRO ALA ASP LYS PRO GLN VAL LEU ALA SER PHE THR SEQRES 2 A 122 GLN THR SER ALA SER SER GLN ASN ALA TRP LEU ALA ALA SEQRES 3 A 122 ASN ARG ASN GLN SER ALA TRP ALA ALA TYR GLU PHE ASP SEQRES 4 A 122 TRP SER THR ASP LEU CYS THR GLN ALA PRO ASP ASN PRO SEQRES 5 A 122 PHE GLY PHE PRO PHE ASN THR ALA CYS ALA ARG HIS ASP SEQRES 6 A 122 PHE GLY TYR ARG ASN TYR LYS ALA ALA GLY SER PHE ASP SEQRES 7 A 122 ALA ASN LYS SER ARG ILE ASP SER ALA PHE TYR GLU ASP SEQRES 8 A 122 MET LYS ARG VAL CYS THR GLY TYR THR GLY GLU LYS ASN SEQRES 9 A 122 THR ALA CYS ASN SER THR ALA TRP THR TYR TYR GLN ALA SEQRES 10 A 122 VAL LYS ILE PHE GLY FORMUL 2 HOH *177(H2 O) HELIX 1 1 ASP A 4 PHE A 12 1 9 HELIX 2 2 SER A 16 ASN A 29 1 14 HELIX 3 3 GLN A 30 GLU A 37 5 8 HELIX 4 4 PHE A 57 GLY A 75 1 19 HELIX 5 5 SER A 76 THR A 97 1 22 HELIX 6 6 THR A 100 ILE A 120 1 21 SSBOND 1 CYS A 45 CYS A 61 1555 1555 2.02 SSBOND 2 CYS A 96 CYS A 107 1555 1555 2.02 CRYST1 29.340 57.495 31.807 90.00 111.07 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 0.034083 0.000000 0.013128 0.00000 SCALE2 0.000000 0.017393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033691 0.00000 MASTER 240 0 0 6 0 0 0 6 0 0 0 10 END