HEADER OXIDOREDUCTASE 13-DEC-14 4XAA TITLE CRYSTAL STRUCTURE OF AVIO1 FROM STREPTOMYCES VIRIDOCHROMOGENES TUE57 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE OXYGENASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VIRIDOCHROMOGENES TUE57; SOURCE 3 ORGANISM_TAXID: 1160705; SOURCE 4 GENE: AVIO1, STVIR_2892; 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: PET23 KEYWDS OXIDOREDUCTASE, DOUBLE STRANDED BETA HELIX EXPDTA X-RAY DIFFRACTION AUTHOR K.M.MCCULLOCH,E.K.MCCRANIE,M.SARWAR,J.L.MATHIEU,B.L.GITSCHLAG,Y.DU, AUTHOR 2 B.O.BACHMANN,T.M.IVERSON REVDAT 4 28-FEB-24 4XAA 1 JRNL REMARK LINK REVDAT 3 30-SEP-15 4XAA 1 JRNL REVDAT 2 19-AUG-15 4XAA 1 JRNL REVDAT 1 05-AUG-15 4XAA 0 JRNL AUTH K.M.MCCULLOCH,E.K.MCCRANIE,J.A.SMITH,M.SARWAR,J.L.MATHIEU, JRNL AUTH 2 B.L.GITSCHLAG,Y.DU,B.O.BACHMANN,T.M.IVERSON JRNL TITL OXIDATIVE CYCLIZATIONS IN ORTHOSOMYCIN BIOSYNTHESIS EXPAND JRNL TITL 2 THE KNOWN CHEMISTRY OF AN OXYGENASE SUPERFAMILY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 11547 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 26240321 JRNL DOI 10.1073/PNAS.1500964112 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10PRE_2083: ???) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 21223 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1081 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 27.0587 - 4.5936 0.85 2469 113 0.1623 0.1717 REMARK 3 2 4.5936 - 3.6489 0.90 2567 151 0.1570 0.1816 REMARK 3 3 3.6489 - 3.1885 0.92 2618 143 0.1881 0.2249 REMARK 3 4 3.1885 - 2.8974 0.94 2714 129 0.2176 0.2709 REMARK 3 5 2.8974 - 2.6899 0.93 2702 124 0.2264 0.2918 REMARK 3 6 2.6899 - 2.5314 0.93 2671 154 0.2299 0.3023 REMARK 3 7 2.5314 - 2.4047 0.89 2490 158 0.2417 0.2796 REMARK 3 8 2.4047 - 2.3001 0.66 1911 109 0.2775 0.2977 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 1745 REMARK 3 ANGLE : 1.104 2392 REMARK 3 CHIRALITY : 0.045 264 REMARK 3 PLANARITY : 0.005 325 REMARK 3 DIHEDRAL : 12.976 641 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4XAA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.485 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CAPS, 1.2 M NAH2PO4, 0.8 M REMARK 280 K2HPO4, 0.2 M LI2SO4, PH 10.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 36.05950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.57200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.05950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.57200 REMARK 290 SMTRY3 4 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: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 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 MET A 1 REMARK 465 THR A 2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 64 N CB CG OD1 OD2 REMARK 480 HIS A 149 CB CG ND1 CD2 CE1 NE2 REMARK 480 ARG A 172 CG CD NE CZ NH1 NH2 REMARK 480 PRO A 223 C O 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 7 78.94 -150.04 REMARK 500 VAL A 26 -45.45 -133.30 REMARK 500 TRP A 80 35.22 -152.45 REMARK 500 ALA A 108 143.55 -173.39 REMARK 500 TYR A 117 -39.70 69.90 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 NI A 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 125 NE2 REMARK 620 2 ASP A 127 OD1 79.3 REMARK 620 3 HIS A 196 NE2 86.1 90.2 REMARK 620 4 HOH A 426 O 172.2 93.0 93.3 REMARK 620 5 HOH A 429 O 100.8 160.5 109.3 86.8 REMARK 620 6 HOH A 440 O 100.5 104.4 164.8 82.1 56.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XAB RELATED DB: PDB REMARK 900 RELATED ID: 4XAC RELATED DB: PDB DBREF 4XAA A 1 223 UNP Q93KW4 Q93KW4_STRVR 1 223 SEQRES 1 A 223 MET THR THR ALA THR LEU ASP ARG ALA ALA ALA ILE GLU SEQRES 2 A 223 ARG PHE ARG ARG ASP GLY PHE ALA ASN ALA GLY PRO VAL SEQRES 3 A 223 LEU ALA PRO ASP ALA ILE ALA ARG LEU LYS ALA GLY ALA SEQRES 4 A 223 GLU ARG LEU ILE THR ARG PHE THR ASP GLU GLY LEU ARG SEQRES 5 A 223 SER ASP ASP TYR TRP ASN PHE PRO VAL GLU GLY ASP GLU SEQRES 6 A 223 ARG PRO VAL LEU TYR ARG VAL HIS ASN LEU GLU LYS GLN SEQRES 7 A 223 ASP TRP ALA PRO GLU ARG ASP LEU LEU HIS ARG GLU GLU SEQRES 8 A 223 LEU ALA GLN LEU ALA ALA ALA PHE VAL ASP GLY PRO VAL SEQRES 9 A 223 VAL PRO THR ALA TYR ALA LEU VAL LEU LYS GLU PRO TYR SEQRES 10 A 223 ARG ALA ALA GLU VAL PRO TRP HIS ARG ASP ARG VAL ASN SEQRES 11 A 223 VAL GLY PRO ARG THR VAL CYS ASN LEU SER ILE CYS LEU SEQRES 12 A 223 ASP ASP ALA GLY PRO HIS ASN GLY CYS LEU GLU ALA VAL SEQRES 13 A 223 PRO GLY SER HIS LEU LEU PRO ASP ASP ALA GLU VAL ALA SEQRES 14 A 223 LYS VAL ARG ALA THR GLY PRO VAL VAL PRO VAL PRO VAL SEQRES 15 A 223 SER GLN GLY ASP VAL VAL VAL HIS ASP VAL ARG LEU VAL SEQRES 16 A 223 HIS GLY SER GLY PRO ASN ALA ASN GLY SER TRP ARG ARG SEQRES 17 A 223 THR ILE VAL ILE GLU TYR ALA ASP PRO ALA ALA PRO PRO SEQRES 18 A 223 ALA PRO HET NI A 301 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *61(H2 O) HELIX 1 AA1 ASP A 7 GLY A 19 1 13 HELIX 2 AA2 ALA A 28 ASP A 48 1 21 HELIX 3 AA3 ASN A 74 GLN A 78 5 5 HELIX 4 AA4 PRO A 82 HIS A 88 5 7 HELIX 5 AA5 ARG A 89 ASP A 101 1 13 HELIX 6 AA6 GLY A 147 GLY A 151 5 5 HELIX 7 AA7 GLY A 158 LEU A 162 5 5 HELIX 8 AA8 GLU A 167 GLY A 175 1 9 SHEET 1 AA1 7 PHE A 20 PRO A 25 0 SHEET 2 AA1 7 ASP A 186 ASP A 191 -1 O VAL A 187 N ALA A 23 SHEET 3 AA1 7 VAL A 136 CYS A 142 -1 N SER A 140 O VAL A 188 SHEET 4 AA1 7 ARG A 207 ALA A 215 -1 O ILE A 212 N LEU A 139 SHEET 5 AA1 7 VAL A 105 LYS A 114 -1 N THR A 107 O GLU A 213 SHEET 6 AA1 7 VAL A 68 VAL A 72 -1 N VAL A 72 O LEU A 111 SHEET 7 AA1 7 TYR A 56 PHE A 59 -1 N PHE A 59 O VAL A 68 SHEET 1 AA2 4 VAL A 122 HIS A 125 0 SHEET 2 AA2 4 HIS A 196 SER A 198 -1 O SER A 198 N VAL A 122 SHEET 3 AA2 4 LEU A 153 ALA A 155 -1 N GLU A 154 O GLY A 197 SHEET 4 AA2 4 VAL A 178 PRO A 179 -1 O VAL A 178 N ALA A 155 LINK NE2 HIS A 125 NI NI A 301 1555 1555 2.25 LINK OD1 ASP A 127 NI NI A 301 1555 1555 2.29 LINK NE2 HIS A 196 NI NI A 301 1555 1555 2.24 LINK NI NI A 301 O HOH A 426 1555 1555 2.22 LINK NI NI A 301 O HOH A 429 1555 1555 2.56 LINK NI NI A 301 O HOH A 440 1555 1555 2.36 CISPEP 1 ALA A 81 PRO A 82 0 4.74 CISPEP 2 GLY A 175 PRO A 176 0 5.60 SITE 1 AC1 6 HIS A 125 ASP A 127 HIS A 196 HOH A 426 SITE 2 AC1 6 HOH A 429 HOH A 440 CRYST1 72.119 115.144 33.864 90.00 90.00 90.00 P 21 21 2 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 0.013866 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029530 0.00000