HEADER HYDROLASE 14-NOV-12 4HYQ TITLE CRYSTAL STRUCTURE OF PHOSPHOLIPASE A1 FROM STREPTOMYCES ALBIDOFLAVUS TITLE 2 NA297 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.32; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES ALBIDOFLAVUS; SOURCE 3 ORGANISM_TAXID: 1886; SOURCE 4 STRAIN: NA297; SOURCE 5 EXPRESSION_SYSTEM: STREPTOMYCES LIVIDANS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1916; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PUC702/PLA KEYWDS LIPASE, GLYCEROPHOSPHOLIPID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.MURAYAMA,D.SUGIMORI REVDAT 2 08-NOV-23 4HYQ 1 REMARK REVDAT 1 29-MAY-13 4HYQ 0 JRNL AUTH K.MURAYAMA,K.KANO,Y.MATSUMOTO,D.SUGIMORI JRNL TITL CRYSTAL STRUCTURE OF PHOSPHOLIPASE A1 FROM STREPTOMYCES JRNL TITL 2 ALBIDOFLAVUS NA297 JRNL REF J.STRUCT.BIOL. V. 182 192 2013 JRNL REFN ISSN 1047-8477 JRNL PMID 23416196 JRNL DOI 10.1016/J.JSB.2013.02.003 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1591373.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1256 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3904 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 197 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1700 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.84000 REMARK 3 B22 (A**2) : 1.84000 REMARK 3 B33 (A**2) : -3.67000 REMARK 3 B12 (A**2) : 1.13000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.10 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.220 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.850 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.070 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.950 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 61.36 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : 1PE.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : 1PE.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4HYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000076086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26008 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 37.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10500 REMARK 200 FOR THE DATA SET : 29.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.61800 REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1ESC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 3% PEGMME2000, REMARK 280 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.03733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.07467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 64.07467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.03733 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 ASP A 10 -158.67 -103.37 REMARK 500 GLN A 97 -164.88 -116.55 REMARK 500 THR A 151 106.77 25.13 REMARK 500 ALA A 154 -15.22 73.22 REMARK 500 LEU A 156 175.14 77.07 REMARK 500 CYS A 199 2.24 82.80 REMARK 500 ASP A 202 51.70 -152.74 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 21 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 301 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE UNP SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT REMARK 999 CURRENTLY EXIST. THIS SEQUENCE HAS BEEN DEPOSITED TO GENBANK, REMARK 999 BAM45317 DBREF 4HYQ A 1 236 PDB 4HYQ 4HYQ 1 236 SEQRES 1 A 236 ALA ALA GLY GLY TYR VAL ALA LEU GLY ASP SER TYR SER SEQRES 2 A 236 SER GLY VAL GLY ALA GLY SER TYR ASP SER GLY SER GLY SEQRES 3 A 236 ASP CYS ARG ARG THR PRO LYS ALA TYR PRO ALA LEU TRP SEQRES 4 A 236 ALA ALA ALA ASN SER PRO ALA SER PHE ASP PHE VAL ALA SEQRES 5 A 236 CYS SER GLY ALA VAL THR SER ASP VAL LEU ASN LYS GLN SEQRES 6 A 236 MET GLY PRO LEU ASN SER SER THR SER LEU VAL SER LEU SEQRES 7 A 236 THR ILE GLY GLY ASN ASP ALA GLY PHE ALA ASP VAL MET SEQRES 8 A 236 THR THR CYS VAL LEU GLN SER GLU ALA ASN CYS ILE ALA SEQRES 9 A 236 ARG VAL ASN THR ALA LYS ALA PHE VAL GLU SER THR LEU SEQRES 10 A 236 PRO GLY ARG LEU ASP SER VAL TYR SER GLN VAL ARG ALA SEQRES 11 A 236 LYS ALA PRO SER ALA ASN VAL VAL VAL LEU GLY TYR PRO SEQRES 12 A 236 ARG PHE TYR LYS LEU ASN GLY THR CYS VAL ALA GLY LEU SEQRES 13 A 236 THR GLU GLY GLU ARG THR ALA ILE ASN GLY ALA ALA ASP SEQRES 14 A 236 LEU LEU ASN SER VAL ILE SER LYS ARG ALA ALA ASP HIS SEQRES 15 A 236 GLY TYR ALA TYR GLY ASP ILE ALA ALA ALA PHE THR GLY SEQRES 16 A 236 HIS GLU ILE CYS SER GLY ASP SER TRP LEU HIS SER VAL SEQRES 17 A 236 LYS TRP THR GLY ILE ASN ASP SER TYR HIS PRO THR ALA SEQRES 18 A 236 ALA GLY GLN SER GLY GLY TYR LEU PRO VAL LEU ASN SER SEQRES 19 A 236 LYS ALA HET 1PE A 301 16 HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 1PE C10 H22 O6 FORMUL 3 HOH *218(H2 O) HELIX 1 1 ASP A 10 GLY A 15 1 6 HELIX 2 2 ASP A 22 ARG A 29 5 8 HELIX 3 3 ALA A 34 SER A 44 1 11 HELIX 4 4 VAL A 57 GLN A 65 1 9 HELIX 5 5 GLY A 86 GLN A 97 1 12 HELIX 6 6 SER A 98 THR A 116 1 19 HELIX 7 7 THR A 116 ALA A 132 1 17 HELIX 8 8 THR A 157 HIS A 182 1 26 HELIX 9 9 ASP A 188 PHE A 193 1 6 HELIX 10 10 THR A 220 GLY A 227 1 8 HELIX 11 11 GLY A 227 ALA A 236 1 10 SHEET 1 A 5 SER A 47 PHE A 50 0 SHEET 2 A 5 GLY A 4 GLY A 9 1 N ALA A 7 O ASP A 49 SHEET 3 A 5 THR A 73 THR A 79 1 O SER A 77 N LEU A 8 SHEET 4 A 5 ASN A 136 LEU A 140 1 O VAL A 138 N VAL A 76 SHEET 5 A 5 ALA A 185 GLY A 187 1 O ALA A 185 N VAL A 139 SSBOND 1 CYS A 28 CYS A 53 1555 1555 2.05 SSBOND 2 CYS A 94 CYS A 102 1555 1555 2.03 SSBOND 3 CYS A 152 CYS A 199 1555 1555 2.03 SITE 1 AC1 11 TYR A 12 SER A 54 GLY A 82 ASN A 83 SITE 2 AC1 11 PHE A 87 ALA A 88 TYR A 142 ASN A 214 SITE 3 AC1 11 SER A 216 HIS A 218 HOH A 503 CRYST1 67.550 67.550 96.112 90.00 90.00 120.00 P 31 2 1 6 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 0.014804 0.008547 0.000000 0.00000 SCALE2 0.000000 0.017094 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010405 0.00000