HEADER OXIDOREDUCTASE 10-JUL-08 3DQY TITLE CRYSTAL STRUCTURE OF TOLUENE 2,3-DIOXYGENASE FERREDOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLUENE 1,2-DIOXYGENASE SYSTEM FERREDOXIN SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 STRAIN: F1; SOURCE 5 GENE: TODB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDTG614 KEYWDS RIESKE, IRON-SULFUR CLUSTER, 2FE-2S, AROMATIC HYDROCARBONS KEYWDS 2 CATABOLISM, ELECTRON TRANSPORT, IRON, IRON-SULFUR, METAL-BINDING, KEYWDS 3 TRANSPORT, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.FRIEMANN,K.LEE,E.N.BROWN,D.T.GIBSON,H.EKLUND,S.RAMASWAMY REVDAT 3 15-NOV-23 3DQY 1 REMARK REVDAT 2 30-AUG-23 3DQY 1 REMARK LINK REVDAT 1 10-MAR-09 3DQY 0 JRNL AUTH R.FRIEMANN,K.LEE,E.N.BROWN,D.T.GIBSON,H.EKLUND,S.RAMASWAMY JRNL TITL STRUCTURES OF THE MULTICOMPONENT RIESKE NON-HEME IRON JRNL TITL 2 TOLUENE 2,3-DIOXYGENASE ENZYME SYSTEM JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 65 24 2009 JRNL REFN ISSN 0907-4449 JRNL PMID 19153463 JRNL DOI 10.1107/S0907444908036524 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 25865 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 + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1368 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 826 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.35000 REMARK 3 B22 (A**2) : -1.37000 REMARK 3 B33 (A**2) : 1.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.69000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.009 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.596 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DQY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048378. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9340 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.1.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27254 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 28.344 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 3.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32800 REMARK 200 R SYM FOR SHELL (I) : 0.32800 REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1FQT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 38% (W/V) PEG 8000, 0.1 M MES, PH 6.1, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 286K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.04500 REMARK 290 SMTRY3 2 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 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 FES A 107 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 42 SG REMARK 620 2 FES A 107 S1 109.2 REMARK 620 3 FES A 107 S2 111.4 105.6 REMARK 620 4 CYS A 61 SG 112.3 109.2 109.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 107 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 44 ND1 REMARK 620 2 FES A 107 S1 121.2 REMARK 620 3 FES A 107 S2 108.6 104.6 REMARK 620 4 HIS A 64 ND1 93.8 106.0 123.8 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 FES A 107 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EF6 RELATED DB: PDB REMARK 900 STRUCTURE OF TOLUENE 2,3-DIOXYGENASE REDUCTASE COMPONENT REMARK 900 RELATED ID: 3EN1 RELATED DB: PDB REMARK 900 STRUCTURE OF THE TOLUENE 2,3-DIOXYGENASE COMPONENT REMARK 900 RELATED ID: 3EQQ RELATED DB: PDB REMARK 900 STRUCTURE OF THE APO-TOLUENE 2,3-DIOXYGENASE COMPONENT DBREF 3DQY A 1 106 UNP P0C620 TODB_PSEPU 2 107 SEQRES 1 A 106 THR TRP THR TYR ILE LEU ARG GLN GLY ASP LEU PRO PRO SEQRES 2 A 106 GLY GLU MET GLN ARG TYR GLU GLY GLY PRO GLU PRO VAL SEQRES 3 A 106 MET VAL CYS ASN VAL ASP GLY GLU PHE PHE ALA VAL GLN SEQRES 4 A 106 ASP THR CYS THR HIS GLY ASP TRP ALA LEU SER ASP GLY SEQRES 5 A 106 TYR LEU ASP GLY ASP ILE VAL GLU CYS THR LEU HIS PHE SEQRES 6 A 106 GLY LYS PHE CSO VAL ARG THR GLY LYS VAL LYS ALA LEU SEQRES 7 A 106 PRO ALA CYS LYS PRO ILE LYS VAL PHE PRO ILE LYS VAL SEQRES 8 A 106 GLU GLY ASP GLU VAL HIS VAL ASP LEU ASP ASN GLY GLU SEQRES 9 A 106 LEU LYS MODRES 3DQY CSO A 69 CYS S-HYDROXYCYSTEINE HET CSO A 69 7 HET FES A 107 4 HETNAM CSO S-HYDROXYCYSTEINE HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 FES FE2 S2 FORMUL 3 HOH *76(H2 O) HELIX 1 1 GLY A 9 LEU A 11 5 3 HELIX 2 2 ALA A 48 GLY A 52 5 5 HELIX 3 3 LEU A 100 GLY A 103 5 4 SHEET 1 A 3 THR A 3 ARG A 7 0 SHEET 2 A 3 GLU A 95 VAL A 98 -1 O VAL A 96 N LEU A 6 SHEET 3 A 3 ILE A 89 GLU A 92 -1 N LYS A 90 O HIS A 97 SHEET 1 B 4 MET A 16 TYR A 19 0 SHEET 2 B 4 VAL A 26 VAL A 31 -1 O VAL A 26 N TYR A 19 SHEET 3 B 4 GLU A 34 GLN A 39 -1 O GLU A 34 N VAL A 31 SHEET 4 B 4 VAL A 86 PHE A 87 -1 O PHE A 87 N ALA A 37 SHEET 1 C 4 TYR A 53 ASP A 55 0 SHEET 2 C 4 ILE A 58 GLU A 60 -1 O ILE A 58 N ASP A 55 SHEET 3 C 4 LYS A 67 CSO A 69 -1 O PHE A 68 N VAL A 59 SHEET 4 C 4 VAL A 75 ALA A 77 -1 O LYS A 76 N LYS A 67 LINK C PHE A 68 N CSO A 69 1555 1555 1.33 LINK C CSO A 69 N VAL A 70 1555 1555 1.33 LINK SG CYS A 42 FE2 FES A 107 1555 1555 2.31 LINK ND1 HIS A 44 FE1 FES A 107 1555 1555 2.11 LINK SG CYS A 61 FE2 FES A 107 1555 1555 2.29 LINK ND1 HIS A 64 FE1 FES A 107 1555 1555 2.08 CISPEP 1 LEU A 78 PRO A 79 0 5.05 SITE 1 AC1 6 CYS A 42 HIS A 44 GLY A 45 CYS A 61 SITE 2 AC1 6 HIS A 64 GLY A 66 CRYST1 30.544 52.090 30.948 90.00 113.67 90.00 P 1 21 1 2 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 0.032740 0.000000 0.014351 0.00000 SCALE2 0.000000 0.019198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035280 0.00000