HEADER HYDROLASE 08-JAN-02 1IT4 TITLE SOLUTION STRUCTURE OF THE PROKARYOTIC PHOSPHOLIPASE A2 FROM TITLE 2 STREPTOMYCES VIOLACEORUBER 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: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROKARYOTIC PLA2, HYDROLASE EXPDTA SOLUTION NMR AUTHOR K.OHTANI,M.SUGIYAMA,M.IZUHARA,T.KOIKE REVDAT 5 27-DEC-23 1IT4 1 REMARK REVDAT 4 23-FEB-22 1IT4 1 REMARK LINK REVDAT 3 24-FEB-09 1IT4 1 VERSN REVDAT 2 01-APR-03 1IT4 1 JRNL REVDAT 1 04-SEP-02 1IT4 0 JRNL AUTH M.SUGIYAMA,K.OHTANI,M.IZUHARA,T.KOIKE,K.SUZUKI,S.IMAMURA, JRNL AUTH 2 H.MISAKI JRNL TITL A NOVEL PROKARYOTIC PHOSPHOLIPASE A2. CHARACTERIZATION, GENE JRNL TITL 2 CLONING, AND SOLUTION STRUCTURE. JRNL REF J.BIOL.CHEM. V. 277 20051 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11897786 JRNL DOI 10.1074/JBC.M200264200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000005253. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 HH TYR A 68 OD1 ASP A 85 1.53 REMARK 500 OD1 ASP A 39 HG SER A 41 1.54 REMARK 500 O ASP A 43 HG1 THR A 46 1.59 REMARK 500 OD2 ASP A 4 HH TYR A 36 1.60 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 28 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 LEU A 44 CB - CA - C ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 HIS A 64 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP A 78 CB - CA - C ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A 83 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 3.4 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 -139.13 54.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 114 0.08 SIDE CHAIN REMARK 500 TYR A 115 0.07 SIDE CHAIN 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 ASP A 43 OD1 REMARK 620 2 LEU A 44 O 83.7 REMARK 620 3 ASP A 65 OD1 99.0 134.4 REMARK 620 4 ASP A 65 OD2 82.2 86.3 49.7 REMARK 620 N 1 2 3 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: 1IT5 RELATED DB: PDB REMARK 900 1IT5 CONTAINS APO-TYPE PLA2 DBREF 1IT4 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+ HELIX 1 1 ASP A 4 THR A 13 1 10 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 1.99 SSBOND 2 CYS A 96 CYS A 107 1555 1555 2.00 LINK OD1 ASP A 43 CA CA A 200 1555 1555 2.34 LINK O LEU A 44 CA CA A 200 1555 1555 2.27 LINK OD1 ASP A 65 CA CA A 200 1555 1555 2.49 LINK OD2 ASP A 65 CA CA A 200 1555 1555 2.49 SITE 1 AC1 3 ASP A 43 LEU A 44 ASP A 65 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000