HEADER HYDROLASE 28-DEC-01 1KP4 TITLE CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2 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: 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, PROKARYOTE, CALCIUM ION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MATOBA,Y.KATSUBE,M.SUGIYAMA REVDAT 4 11-OCT-17 1KP4 1 REMARK REVDAT 3 24-FEB-09 1KP4 1 VERSN REVDAT 2 01-APR-03 1KP4 1 JRNL REVDAT 1 04-SEP-02 1KP4 0 JRNL AUTH Y.MATOBA,Y.KATSUBE,M.SUGIYAMA JRNL TITL THE CRYSTAL STRUCTURE OF PROKARYOTIC PHOSPHOLIPASE A2. JRNL REF J.BIOL.CHEM. V. 277 20059 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11897785 JRNL DOI 10.1074/JBC.M200263200 REMARK 1 REMARK 1 REFERENCE 1 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. CHARACTERIZATION, 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 76.3 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) : 0.150 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) : 12244 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.144 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)) : 10609 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 : 1 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1047.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4191 REMARK 3 NUMBER OF RESTRAINTS : 3988 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.021 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.045 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.048 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.007 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.041 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KP4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 292 REMARK 200 PH : 8.5 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12820 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 73.2 REMARK 200 DATA REDUNDANCY : 2.370 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.410 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO 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 (%): 47.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, TRIS-HCL, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 297K 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 27.12500 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: THE BIOLOGICAL UNIT OF THIS PROTEIN IS A MONOMER 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 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.1 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 -137.80 54.02 REMARK 500 REMARK 500 REMARK: NULL 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 200 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 203 O REMARK 620 2 HOH A 202 O 76.9 REMARK 620 3 ASP A 65 OD1 116.3 165.8 REMARK 620 4 ASP A 65 OD2 71.2 137.4 50.5 REMARK 620 5 HOH A 201 O 105.4 87.6 84.0 74.8 REMARK 620 6 ASP A 43 OD2 88.0 107.1 79.6 99.4 162.3 REMARK 620 7 LEU A 44 O 153.3 81.8 86.7 135.1 89.5 82.9 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 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FAZ RELATED DB: PDB REMARK 900 1FAZ CONTAINS CALCIUM-FREE FORM OF PROKARYOTIC PHOSPHOLIPASE A2 REMARK 900 RELATED ID: 1IT4 RELATED DB: PDB REMARK 900 1IT4 CONTAINS SOLUTION STRUCTURE OF CALCIUM-BOUND FORM OF REMARK 900 PROKARYOTIC PHOSPHOLIPASE A2 REMARK 900 RELATED ID: 1IT5 RELATED DB: PDB REMARK 900 1IT5 CONTAINS SOLUTION STRUCTURE OF CALCIUM-FREE FORM OF REMARK 900 PROKARYOTIC PHOSPHOLIPASE A2 DBREF 1KP4 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 HET CA A 200 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *88(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 GLY A 122 1 23 SSBOND 1 CYS A 45 CYS A 61 1555 1555 2.01 SSBOND 2 CYS A 96 CYS A 107 1555 1555 2.01 LINK CA CA A 200 O HOH A 203 1555 1555 2.41 LINK CA CA A 200 O HOH A 202 1555 1555 2.40 LINK CA CA A 200 OD1 ASP A 65 1555 1555 2.50 LINK CA CA A 200 OD2 ASP A 65 1555 1555 2.51 LINK CA CA A 200 O HOH A 201 1555 1555 2.32 LINK CA CA A 200 OD2 ASP A 43 1555 1555 2.41 LINK CA CA A 200 O LEU A 44 1555 1555 2.32 SITE 1 AC1 6 ASP A 43 LEU A 44 ASP A 65 HOH A 201 SITE 2 AC1 6 HOH A 202 HOH A 203 CRYST1 38.280 54.250 30.650 90.00 90.20 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 0.026123 0.000000 0.000091 0.00000 SCALE2 0.000000 0.018433 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032627 0.00000 MASTER 245 0 1 6 0 0 2 6 0 0 0 10 END