HEADER HYDROLASE 31-MAY-11 3S8Y TITLE BROMIDE SOAKED STRUCTURE OF AN ESTERASE FROM THE OIL-DEGRADING TITLE 2 BACTERIUM OLEISPIRA ANTARCTICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ESTERASE APC40077; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OLEISPIRA ANTARCTICA; SOURCE 3 ORGANISM_TAXID: 188908; SOURCE 4 GENE: OLEI01171; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P15TV LIC KEYWDS ROSSMANN FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.PETIT,A.DONG,O.KAGAN,A.SAVCHENKO,A.F.YAKUNIN REVDAT 3 13-SEP-23 3S8Y 1 REMARK REVDAT 2 18-JUL-12 3S8Y 1 JRNL VERSN REVDAT 1 15-JUN-11 3S8Y 0 JRNL AUTH S.LEMAK,A.TCHIGVINTSEV,P.PETIT,R.FLICK,A.U.SINGER,G.BROWN, JRNL AUTH 2 E.EVDOKIMOVA,O.EGOROVA,C.F.GONZALEZ,T.N.CHERNIKOVA, JRNL AUTH 3 M.M.YAKIMOV,M.KUBE,R.REINHARDT,P.N.GOLYSHIN,A.SAVCHENKO, JRNL AUTH 4 A.F.YAKUNIN JRNL TITL STRUCTURE AND ACTIVITY OF THE COLD-ACTIVE AND JRNL TITL 2 ANION-ACTIVATED CARBOXYL ESTERASE OLEI01171 FROM THE JRNL TITL 3 OIL-DEGRADING MARINE BACTERIUM OLEISPIRA ANTARCTICA. JRNL REF BIOCHEM.J. V. 445 193 2012 JRNL REFN ISSN 0264-6021 JRNL PMID 22519667 JRNL DOI 10.1042/BJ20112113 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 19117 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 959 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.6964 - 4.0075 0.98 2796 141 0.1775 0.1800 REMARK 3 2 4.0075 - 3.1852 0.99 2715 135 0.1369 0.1620 REMARK 3 3 3.1852 - 2.7838 0.97 2631 147 0.1405 0.1617 REMARK 3 4 2.7838 - 2.5299 0.96 2583 151 0.1407 0.2094 REMARK 3 5 2.5299 - 2.3489 0.95 2537 132 0.1512 0.2008 REMARK 3 6 2.3489 - 2.2106 0.91 2445 126 0.1623 0.2041 REMARK 3 7 2.2106 - 2.1000 0.92 2451 127 0.1681 0.2302 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 45.68 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.42640 REMARK 3 B22 (A**2) : 2.59640 REMARK 3 B33 (A**2) : -7.02280 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2222 REMARK 3 ANGLE : 1.043 3026 REMARK 3 CHIRALITY : 0.073 314 REMARK 3 PLANARITY : 0.004 402 REMARK 3 DIHEDRAL : 12.684 787 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -4.8407 15.6966 -7.7503 REMARK 3 T TENSOR REMARK 3 T11: 0.0532 T22: 0.0550 REMARK 3 T33: 0.0594 T12: 0.0008 REMARK 3 T13: 0.0020 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.2087 L22: 0.2956 REMARK 3 L33: 0.4278 L12: -0.0883 REMARK 3 L13: 0.0117 L23: -0.1561 REMARK 3 S TENSOR REMARK 3 S11: -0.0023 S12: 0.0109 S13: 0.0095 REMARK 3 S21: -0.0010 S22: -0.0015 S23: 0.0218 REMARK 3 S31: 0.0073 S32: -0.0326 S33: 0.0012 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3S8Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000065910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 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 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19720 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 19.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : 0.27000 REMARK 200 FOR SHELL : 6.300 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 3I6Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4M DI-AMMONIUM CITRATE, 22% PEG3350, REMARK 280 SOAKING STEP: KBR 0.8M, 30S. , PH 4.8, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.22550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.02550 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.22550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.02550 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 ALA A 279 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 24 CG OD1 ND2 REMARK 470 GLU A 163 CD OE1 OE2 REMARK 470 LYS A 193 CE NZ REMARK 470 LYS A 211 CG CD CE NZ 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 THR A 56 -4.07 76.02 REMARK 500 SER A 58 -162.94 -100.52 REMARK 500 ALA A 103 47.51 -152.05 REMARK 500 PHE A 105 14.91 56.56 REMARK 500 ASN A 126 -60.60 -107.63 REMARK 500 SER A 148 -124.14 58.55 REMARK 500 ASP A 256 -153.79 -108.07 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 BR A 280 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I6Y RELATED DB: PDB REMARK 900 APO-STATE ENZYME DBREF 3S8Y A 0 279 UNP D0VWZ4 D0VWZ4_OLEAN 1 280 SEQRES 1 A 280 GLY MET SER ILE GLU ASN LEU SER SER ASN LYS SER PHE SEQRES 2 A 280 GLY GLY TRP HIS LYS GLN TYR SER HIS VAL SER ASN THR SEQRES 3 A 280 LEU ASN CYS ALA MET ARG PHE ALA ILE TYR LEU PRO PRO SEQRES 4 A 280 GLN ALA SER THR GLY ALA LYS VAL PRO VAL LEU TYR TRP SEQRES 5 A 280 LEU SER GLY LEU THR CYS SER ASP GLU ASN PHE MET GLN SEQRES 6 A 280 LYS ALA GLY ALA GLN ARG LEU ALA ALA GLU LEU GLY ILE SEQRES 7 A 280 ALA ILE VAL ALA PRO ASP THR SER PRO ARG GLY GLU GLY SEQRES 8 A 280 VAL ALA ASP ASP GLU GLY TYR ASP LEU GLY GLN GLY ALA SEQRES 9 A 280 GLY PHE TYR VAL ASN ALA THR GLN ALA PRO TRP ASN ARG SEQRES 10 A 280 HIS TYR GLN MET TYR ASP TYR VAL VAL ASN GLU LEU PRO SEQRES 11 A 280 GLU LEU ILE GLU SER MET PHE PRO VAL SER ASP LYS ARG SEQRES 12 A 280 ALA ILE ALA GLY HIS SER MET GLY GLY HIS GLY ALA LEU SEQRES 13 A 280 THR ILE ALA LEU ARG ASN PRO GLU ARG TYR GLN SER VAL SEQRES 14 A 280 SER ALA PHE SER PRO ILE ASN ASN PRO VAL ASN CYS PRO SEQRES 15 A 280 TRP GLY GLN LYS ALA PHE THR ALA TYR LEU GLY LYS ASP SEQRES 16 A 280 THR ASP THR TRP ARG GLU TYR ASP ALA SER LEU LEU MET SEQRES 17 A 280 ARG ALA ALA LYS GLN TYR VAL PRO ALA LEU VAL ASP GLN SEQRES 18 A 280 GLY GLU ALA ASP ASN PHE LEU ALA GLU GLN LEU LYS PRO SEQRES 19 A 280 GLU VAL LEU GLU ALA ALA ALA SER SER ASN ASN TYR PRO SEQRES 20 A 280 LEU GLU LEU ARG SER HIS GLU GLY TYR ASP HIS SER TYR SEQRES 21 A 280 TYR PHE ILE ALA SER PHE ILE GLU ASP HIS LEU ARG PHE SEQRES 22 A 280 HIS SER ASN TYR LEU ASN ALA HET BR A 280 1 HETNAM BR BROMIDE ION FORMUL 2 BR BR 1- FORMUL 3 HOH *181(H2 O) HELIX 1 1 PRO A 37 THR A 42 5 6 HELIX 2 2 GLU A 60 ALA A 66 1 7 HELIX 3 3 ALA A 68 GLY A 76 1 9 HELIX 4 4 PRO A 113 HIS A 117 5 5 HELIX 5 5 GLN A 119 ASN A 126 1 8 HELIX 6 6 ASN A 126 PHE A 136 1 11 HELIX 7 7 SER A 148 ASN A 161 1 14 HELIX 8 8 ASN A 176 ASN A 179 5 4 HELIX 9 9 CYS A 180 GLY A 192 1 13 HELIX 10 10 ASP A 194 TYR A 201 5 8 HELIX 11 11 ASP A 202 ALA A 210 1 9 HELIX 12 12 LYS A 232 SER A 242 1 11 HELIX 13 13 SER A 258 ASN A 278 1 21 SHEET 1 A 9 ILE A 3 SER A 11 0 SHEET 2 A 9 GLY A 14 SER A 23 -1 O SER A 20 N GLU A 4 SHEET 3 A 9 CYS A 28 LEU A 36 -1 O PHE A 32 N TYR A 19 SHEET 4 A 9 ALA A 78 PRO A 82 -1 O ALA A 81 N ALA A 33 SHEET 5 A 9 VAL A 46 LEU A 52 1 N TRP A 51 O VAL A 80 SHEET 6 A 9 VAL A 138 HIS A 147 1 O ALA A 145 N LEU A 52 SHEET 7 A 9 VAL A 168 PHE A 171 1 O PHE A 171 N GLY A 146 SHEET 8 A 9 ALA A 216 GLY A 221 1 O ASP A 219 N ALA A 170 SHEET 9 A 9 LEU A 247 HIS A 252 1 O ARG A 250 N VAL A 218 CISPEP 1 ALA A 112 PRO A 113 0 -3.71 SITE 1 AC1 5 GLY A 54 LEU A 55 SER A 148 MET A 149 SITE 2 AC1 5 HOH A 434 CRYST1 44.532 84.451 88.051 90.00 90.00 90.00 P 2 21 21 4 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 0.022456 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011841 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011357 0.00000