10 20 30 40 50 60 70 80 1KP4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 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 JRNL TITL 2 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, REMARK 1 AUTH 2 S.IMAMURA,H.MISAKI REMARK 1 TITL A NOVEL PROKARYOTIC PHOSPHOLIPASE A2. REMARK 1 TITL 2 CHARACTERIZATION, GENE CLONING, AND SOLUTION REMARK 1 TITL 3 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)) : 0.143 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 : 1047.00 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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-02. REMARK 100 THE RCSB ID CODE IS RCSB015191.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 REMARK 900 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