HEADER METAL BINDING PROTEIN 07-MAY-13 3WAQ TITLE HEMERYTHRIN-LIKE DOMAIN OF DCRH I119E MUTANT (MET) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMERYTHRIN-LIKE DOMAIN PROTEIN DCRH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 882; SOURCE 4 STRAIN: HILDENBOROUGH; SOURCE 5 GENE: DCRH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-16B KEYWDS METAL-BINDING, HELIX BUNDLE, METAL BINDING PROTEIN, OXYGEN SENSOR EXPDTA X-RAY DIFFRACTION AUTHOR Y.OKAMOTO,A.ONODA,H.SUGIMOTO,Y.TAKANO,S.HIROTA,D.M.KURTZ JR.,Y.SHIRO, AUTHOR 2 T.HAYASHI REVDAT 2 08-NOV-23 3WAQ 1 REMARK SEQADV LINK REVDAT 1 19-MAR-14 3WAQ 0 JRNL AUTH Y.OKAMOTO,A.ONODA,H.SUGIMOTO,Y.TAKANO,S.HIROTA, JRNL AUTH 2 D.M.KURTZ JR.,Y.SHIRO,T.HAYASHI JRNL TITL CRYSTAL STRUCTURE, EXOGENOUS LIGAND BINDING, AND REDOX JRNL TITL 2 PROPERTIES OF AN ENGINEERED DIIRON ACTIVE SITE IN A JRNL TITL 3 BACTERIAL HEMERYTHRIN JRNL REF INORG.CHEM. V. 52 13014 2013 JRNL REFN ISSN 0020-1669 JRNL PMID 24187962 JRNL DOI 10.1021/IC401632X REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 21644 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1066 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 19.7127 - 3.5850 0.99 2601 120 0.2071 0.2581 REMARK 3 2 3.5850 - 2.8483 1.00 2576 126 0.2071 0.2323 REMARK 3 3 2.8483 - 2.4891 1.00 2605 145 0.2078 0.2595 REMARK 3 4 2.4891 - 2.2618 1.00 2559 163 0.1896 0.2758 REMARK 3 5 2.2618 - 2.0999 1.00 2633 118 0.1957 0.2424 REMARK 3 6 2.0999 - 1.9762 1.00 2547 141 0.2197 0.2708 REMARK 3 7 1.9762 - 1.8773 0.99 2593 122 0.2226 0.3235 REMARK 3 8 1.8773 - 1.7957 0.96 2464 131 0.2241 0.3144 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 : 0.36 REMARK 3 B_SOL : 47.69 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.61560 REMARK 3 B22 (A**2) : -0.12200 REMARK 3 B33 (A**2) : -9.49360 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 : 0.015 1190 REMARK 3 ANGLE : 1.322 1629 REMARK 3 CHIRALITY : 0.082 169 REMARK 3 PLANARITY : 0.006 207 REMARK 3 DIHEDRAL : 16.091 454 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 4:70) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4328 5.9578 21.6186 REMARK 3 T TENSOR REMARK 3 T11: 0.1333 T22: 0.1324 REMARK 3 T33: 0.1552 T12: -0.0192 REMARK 3 T13: 0.0031 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 0.9846 L22: 2.6646 REMARK 3 L33: 3.1489 L12: 0.0021 REMARK 3 L13: 0.0323 L23: -1.5080 REMARK 3 S TENSOR REMARK 3 S11: 0.0451 S12: -0.0959 S13: -0.0496 REMARK 3 S21: 0.2828 S22: -0.1205 S23: -0.2480 REMARK 3 S31: 0.0147 S32: 0.1469 S33: 0.1130 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 71:201) REMARK 3 ORIGIN FOR THE GROUP (A): 3.7165 11.8105 18.6489 REMARK 3 T TENSOR REMARK 3 T11: 0.1438 T22: 0.1029 REMARK 3 T33: 0.1792 T12: 0.0166 REMARK 3 T13: 0.0511 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 2.6431 L22: 3.4183 REMARK 3 L33: 2.3826 L12: -0.2514 REMARK 3 L13: -0.3028 L23: -0.2858 REMARK 3 S TENSOR REMARK 3 S11: -0.0677 S12: 0.0366 S13: 0.1469 REMARK 3 S21: 0.4806 S22: 0.1038 S23: 0.3561 REMARK 3 S31: -0.0173 S32: -0.3185 S33: -0.0445 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SF FILE CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 3WAQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000096099. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23644 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 25.0540 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.27900 REMARK 200 R SYM FOR SHELL (I) : 0.27900 REMARK 200 FOR SHELL : 4.895 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: 3AGT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MOPS, 50MG/ML PROTEIN, PH 7.0, REMARK 280 SMALL TUBES, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.48250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.33850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.42950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.33850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.48250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.42950 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 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 1 REMARK 465 ASP A 2 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 ASN A 15 -150.77 -151.03 REMARK 500 ASP A 41 95.82 -165.74 REMARK 500 HIS A 118 -63.44 -99.80 REMARK 500 MET A 120 -74.86 -87.65 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 FEO A 201 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 23 NE2 REMARK 620 2 FEO A 201 O 176.7 REMARK 620 3 HIS A 59 NE2 82.7 95.7 REMARK 620 4 GLU A 63 OE2 91.3 91.3 83.4 REMARK 620 5 GLU A 119 OE1 75.5 102.0 99.1 166.1 REMARK 620 6 ASP A 123 OD2 80.6 101.5 160.0 86.2 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FEO A 201 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 63 OE1 REMARK 620 2 FEO A 201 O 88.6 REMARK 620 3 HIS A 78 NE2 87.1 175.6 REMARK 620 4 HIS A 82 NE2 89.1 92.9 86.0 REMARK 620 5 HIS A 118 NE2 175.6 94.8 89.4 87.9 REMARK 620 6 ASP A 123 OD1 91.5 100.7 80.5 166.5 90.7 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 FEO A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ATG RELATED DB: PDB REMARK 900 WILD TYPE IN MET FORM REMARK 900 RELATED ID: 3AGU RELATED DB: PDB REMARK 900 WILD TYPE IN SEMIMET-R FORM DBREF 3WAQ A 1 136 UNP Q9REU3 Q9REU3_DESVU 1 136 SEQADV 3WAQ GLU A 119 UNP Q9REU3 ILE 119 ENGINEERED MUTATION SEQRES 1 A 136 GLY ASP ALA ASP VAL LEU VAL LYS TRP SER GLU ASP LEU SEQRES 2 A 136 ALA ASN LEU PRO SER ILE ASP THR GLN HIS LYS ARG LEU SEQRES 3 A 136 VAL ASP TYR ILE ASN ASP LEU TYR ARG ALA ALA ARG ARG SEQRES 4 A 136 ARG ASP MET ASP LYS ALA ARG GLU VAL PHE ASP ALA LEU SEQRES 5 A 136 LYS ASN TYR ALA VAL GLU HIS PHE GLY TYR GLU GLU ARG SEQRES 6 A 136 LEU PHE ALA ASP TYR ALA TYR PRO GLU ALA THR ARG HIS SEQRES 7 A 136 LYS GLU ILE HIS ARG ARG PHE VAL GLU THR VAL LEU LYS SEQRES 8 A 136 TRP GLU LYS GLN LEU ALA ALA GLY ASP PRO GLU VAL VAL SEQRES 9 A 136 MET THR THR LEU ARG GLY LEU VAL ASP TRP LEU VAL ASN SEQRES 10 A 136 HIS GLU MET LYS GLU ASP LYS LYS TYR GLU ALA TYR LEU SEQRES 11 A 136 ARG GLU ARG GLY VAL SER HET FEO A 201 3 HETNAM FEO MU-OXO-DIIRON FORMUL 2 FEO FE2 O FORMUL 3 HOH *57(H2 O) HELIX 1 1 LEU A 16 ARG A 40 1 25 HELIX 2 2 ASP A 41 ALA A 71 1 31 HELIX 3 3 GLU A 74 LEU A 96 1 23 HELIX 4 4 GLU A 102 HIS A 118 1 17 HELIX 5 5 MET A 120 LYS A 125 1 6 HELIX 6 6 TYR A 126 ARG A 133 1 8 LINK NE2 HIS A 23 FE2 FEO A 201 1555 1555 2.37 LINK NE2 HIS A 59 FE2 FEO A 201 1555 1555 2.08 LINK OE1 GLU A 63 FE1 FEO A 201 1555 1555 2.11 LINK OE2 GLU A 63 FE2 FEO A 201 1555 1555 2.26 LINK NE2 HIS A 78 FE1 FEO A 201 1555 1555 2.26 LINK NE2 HIS A 82 FE1 FEO A 201 1555 1555 2.27 LINK NE2 HIS A 118 FE1 FEO A 201 1555 1555 2.10 LINK OE1 GLU A 119 FE2 FEO A 201 1555 1555 2.07 LINK OD2 ASP A 123 FE2 FEO A 201 1555 1555 2.03 LINK OD1 ASP A 123 FE1 FEO A 201 1555 1555 2.26 CISPEP 1 ARG A 39 ARG A 40 0 -9.75 CISPEP 2 ALA A 97 ALA A 98 0 -5.80 SITE 1 AC1 9 HIS A 23 HIS A 59 PHE A 60 GLU A 63 SITE 2 AC1 9 HIS A 78 HIS A 82 HIS A 118 GLU A 119 SITE 3 AC1 9 ASP A 123 CRYST1 30.965 50.859 76.677 90.00 90.00 90.00 P 21 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 0.032295 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019662 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013042 0.00000