HEADER OXIDOREDUCTASE 08-APR-09 3GZX TITLE CRYSTAL STRUCTURE OF THE BIPHENYL DIOXYGENASE IN COMPLEX WITH BIPHENYL TITLE 2 FROM COMAMONAS TESTOSTERONI SP. STRAIN B-356 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIPHENYL DIOXYGENASE SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BIPHENYL 2,3-DIOXYGENASE; COMPND 5 EC: 1.14.12.18; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BIPHENYL DIOXYGENASE SUBUNIT BETA; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: BIPHENYL 2,3-DIOXYGENASE; COMPND 11 EC: 1.14.12.18; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COMAMONAS TESTOSTERONI; SOURCE 3 ORGANISM_COMMON: PSEUDOMONAS TESTOSTERONI; SOURCE 4 ORGANISM_TAXID: 285; SOURCE 5 GENE: BPHA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: COMAMONAS TESTOSTERONI; SOURCE 10 ORGANISM_COMMON: PSEUDOMONAS TESTOSTERONI; SOURCE 11 ORGANISM_TAXID: 285; SOURCE 12 GENE: BPHE; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIOXYGENASE, RIESKIE, NON-HEME IRON, AROMATIC HYDROCARBONS KEYWDS 2 CATABOLISM, IRON, IRON-SULFUR, METAL-BINDING, NAD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.KUMAR,C.L.COLBERT,J.T.BOLIN REVDAT 4 01-NOV-23 3GZX 1 REMARK LINK REVDAT 3 01-NOV-17 3GZX 1 REMARK REVDAT 2 06-FEB-13 3GZX 1 JRNL VERSN REVDAT 1 05-MAY-10 3GZX 0 JRNL AUTH C.L.COLBERT,N.Y.AGAR,P.KUMAR,M.N.CHAKKO,S.C.SINHA, JRNL AUTH 2 J.B.POWLOWSKI,L.D.ELTIS,J.T.BOLIN JRNL TITL STRUCTURAL CHARACTERIZATION OF PANDORAEA PNOMENUSA B-356 JRNL TITL 2 BIPHENYL DIOXYGENASE REVEALS FEATURES OF POTENT JRNL TITL 3 POLYCHLORINATED BIPHENYL-DEGRADING ENZYMES JRNL REF PLOS ONE V. 8 52550 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23308114 JRNL DOI 10.1371/JOURNAL.PONE.0052550 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 91502 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4823 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4249 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3710 REMARK 3 BIN FREE R VALUE SET COUNT : 217 REMARK 3 BIN FREE R VALUE : 0.4050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5023 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.85000 REMARK 3 B22 (A**2) : -0.85000 REMARK 3 B33 (A**2) : 1.27000 REMARK 3 B12 (A**2) : -0.42000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.381 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5286 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7194 ; 0.871 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 651 ; 4.816 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;32.853 ;23.678 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 863 ;12.205 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ; 7.511 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 757 ; 0.059 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4113 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2603 ; 0.146 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3589 ; 0.293 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 679 ; 0.056 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.025 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 172 ; 0.119 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 61 ; 0.071 ; 0.200 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): 3271 ; 0.122 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5110 ; 0.215 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2352 ; 0.230 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2068 ; 0.362 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3GZX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052516. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94792 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : 0.37300 REMARK 200 FOR SHELL : 2.800 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: PDB ENTRY 3GZY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-15% PEG 4000, 100MM MES, 10-15% 2 REMARK 280 -PROPANOL, SODIUM CHLORIDE, PH 6.00, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 68.17750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.36230 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.71833 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 68.17750 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 39.36230 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.71833 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 68.17750 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 39.36230 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.71833 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 78.72460 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 71.43667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 78.72460 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 71.43667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 78.72460 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 71.43667 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 36050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 57070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -205.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 68.17750 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 118.08689 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -68.17750 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 118.08689 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 540 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 589 LIES ON A SPECIAL POSITION. 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 SER A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 MET A 5 REMARK 465 LYS A 6 REMARK 465 ASP A 7 REMARK 465 THR A 8 REMARK 465 GLN A 9 REMARK 465 GLU A 10 REMARK 465 ALA A 11 REMARK 465 PRO A 12 REMARK 465 VAL A 13 REMARK 465 ARG A 14 REMARK 465 TRP A 15 REMARK 465 SER A 16 REMARK 465 ARG A 17 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 ASN A 261 CA CB CG OD1 ND2 REMARK 480 MET A 397 CG SD CE REMARK 480 MET B 56 CG SD CE 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 VAL A 53 -67.81 -108.94 REMARK 500 ARG A 56 15.11 -144.98 REMARK 500 THR A 76 -159.59 -146.03 REMARK 500 ASP A 145 -70.25 -92.60 REMARK 500 SER A 188 -129.84 54.29 REMARK 500 SER A 229 -3.67 -146.41 REMARK 500 ASP A 230 76.56 -107.82 REMARK 500 THR A 236 -97.18 -109.78 REMARK 500 GLN A 257 -116.52 -66.62 REMARK 500 LEU A 258 -71.22 -160.77 REMARK 500 SER A 259 121.75 106.82 REMARK 500 LYS A 260 -2.96 -144.23 REMARK 500 LEU B 139 -131.88 52.83 REMARK 500 SER B 175 -71.69 -96.96 REMARK 500 LEU B 182 54.88 -116.62 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 FES A 700 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 100 SG REMARK 620 2 FES A 700 S1 105.9 REMARK 620 3 FES A 700 S2 112.9 95.3 REMARK 620 4 CYS A 120 SG 115.4 112.0 113.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 700 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 102 ND1 REMARK 620 2 FES A 700 S1 120.2 REMARK 620 3 FES A 700 S2 116.0 95.2 REMARK 620 4 HIS A 123 ND1 93.7 114.7 119.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 701 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 233 NE2 REMARK 620 2 HIS A 239 NE2 96.2 REMARK 620 3 ASP A 386 OD1 92.7 90.0 REMARK 620 4 ASP A 386 OD2 147.4 92.0 55.7 REMARK 620 5 HOH A 458 O 119.5 80.0 146.9 93.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BNL A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 704 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GZY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BIPHENYL DIOXYGENASE FROM COMAMONAS REMARK 900 TESTOSTERONI SP. STRAIN B-356 REMARK 900 RELATED ID: 3GZZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BIPHENYL DIOXYGENASE IN COMPLEX WITH REMARK 900 PHENYLCYCLOHEXADIENEDIOL FROM COMAMONAS TESTOSTERONI SP. STRAIN B- REMARK 900 356 DBREF 3GZX A 1 457 UNP Q46372 BPHA_COMTE 1 457 DBREF 3GZX B 1 186 UNP Q46373 BPHE_COMTE 1 186 SEQRES 1 A 457 MET SER SER THR MET LYS ASP THR GLN GLU ALA PRO VAL SEQRES 2 A 457 ARG TRP SER ARG ASN TRP THR PRO ASP ALA ILE ARG ALA SEQRES 3 A 457 LEU VAL ASP GLN ASP ASN GLY LYS LEU ASP ALA ARG ILE SEQRES 4 A 457 TYR ALA ASP GLN ASP LEU TYR GLN LEU GLU LEU GLU ARG SEQRES 5 A 457 VAL PHE GLY ARG SER TRP LEU MET LEU GLY HIS GLU THR SEQRES 6 A 457 HIS ILE PRO LYS ILE GLY ASP TYR LEU THR THR TYR MET SEQRES 7 A 457 GLY GLU ASP PRO VAL ILE MET VAL ARG GLN LYS ASP GLN SEQRES 8 A 457 SER ILE LYS VAL PHE LEU ASN GLN CYS ARG HIS ARG GLY SEQRES 9 A 457 MET ARG ILE VAL ARG SER ASP GLY GLY ASN ALA LYS ALA SEQRES 10 A 457 PHE THR CYS THR TYR HIS GLY TRP ALA TYR ASP ILE ALA SEQRES 11 A 457 GLY ASN LEU VAL ASN VAL PRO PHE GLU LYS GLU ALA PHE SEQRES 12 A 457 CYS ASP LYS LYS GLU GLY ASP CYS GLY PHE ASP LYS ALA SEQRES 13 A 457 ASP TRP GLY PRO LEU GLN ALA ARG VAL GLU THR TYR LYS SEQRES 14 A 457 GLY LEU VAL PHE ALA ASN TRP ASP PRO GLU ALA PRO ASP SEQRES 15 A 457 LEU LYS THR TYR LEU SER ASP ALA MET PRO TYR MET ASP SEQRES 16 A 457 VAL MET LEU ASP ARG THR GLU ALA GLY THR GLU ALA ILE SEQRES 17 A 457 GLY GLY ILE GLN LYS TRP VAL ILE PRO CYS ASN TRP LYS SEQRES 18 A 457 PHE ALA ALA GLU GLN PHE CYS SER ASP MET TYR HIS ALA SEQRES 19 A 457 GLY THR MET SER HIS LEU SER GLY VAL LEU ALA GLY LEU SEQRES 20 A 457 PRO PRO GLU MET ASP LEU THR GLN ILE GLN LEU SER LYS SEQRES 21 A 457 ASN GLY ASN GLN PHE ARG SER ALA TRP GLY GLY HIS GLY SEQRES 22 A 457 ALA GLY TRP PHE ILE ASN ASP SER SER ILE LEU LEU SER SEQRES 23 A 457 VAL VAL GLY PRO LYS ILE THR GLN TYR TRP THR GLN GLY SEQRES 24 A 457 PRO ALA ALA GLU LYS ALA ALA ARG ARG VAL PRO GLN LEU SEQRES 25 A 457 PRO ILE LEU ASP MET PHE GLY GLN HIS MET THR VAL PHE SEQRES 26 A 457 PRO THR CYS SER PHE LEU PRO GLY ILE ASN THR ILE ARG SEQRES 27 A 457 THR TRP HIS PRO ARG GLY PRO ASN GLU VAL GLU VAL TRP SEQRES 28 A 457 ALA PHE VAL LEU VAL ASP ALA ASP ALA PRO GLU ASP ILE SEQRES 29 A 457 LYS GLU GLU PHE ARG LEU GLN ASN ILE ARG THR PHE ASN SEQRES 30 A 457 ALA GLY GLY VAL PHE GLU GLN ASP ASP GLY GLU ASN TRP SEQRES 31 A 457 VAL GLU ILE GLN ARG VAL MET ARG GLY HIS LYS ALA LYS SEQRES 32 A 457 SER THR SER LEU CYS ALA LYS MET GLY LEU ASN VAL PRO SEQRES 33 A 457 ASN LYS ASN ASN PRO ALA TYR PRO GLY LYS THR ALA TYR SEQRES 34 A 457 VAL TYR ALA GLU GLU ALA ALA ARG GLY MET TYR HIS HIS SEQRES 35 A 457 TRP SER ARG MET MET SER GLU PRO SER TRP ASP THR LEU SEQRES 36 A 457 LYS PRO SEQRES 1 B 186 MET ILE SER THR PRO LEU SER LYS GLU PHE GLU TRP PRO SEQRES 2 B 186 ALA LYS PRO VAL SER LEU GLU LEU GLN HIS GLN VAL GLU SEQRES 3 B 186 GLN PHE TYR TYR ARG GLU ALA GLN LEU LEU ASP HIS HIS SEQRES 4 B 186 ALA PHE GLN ALA TRP PHE ALA LEU LEU ALA GLU ASP ILE SEQRES 5 B 186 HIS TYR TRP MET PRO ILE ARG THR VAL ARG THR ALA ARG SEQRES 6 B 186 GLU GLN GLY LEU GLU TYR VAL PRO ALA GLY ALA ASN ALA SEQRES 7 B 186 HIS PHE ASP ASP THR HIS ALA THR MET TYR GLY ARG ILE SEQRES 8 B 186 ARG GLN LYS THR SER ASP LEU ASN TRP ALA GLU ASP PRO SEQRES 9 B 186 PRO SER ARG THR ARG HIS LEU VAL SER ASN VAL ILE VAL SEQRES 10 B 186 ARG GLU MET ASP THR PRO GLY THR LEU GLU VAL ALA SER SEQRES 11 B 186 ALA PHE LEU LEU TYR ARG SER ARG LEU GLU ARG GLN VAL SEQRES 12 B 186 ASP VAL PHE ALA GLY GLU ARG ARG ASP VAL LEU ARG ILE SEQRES 13 B 186 ALA ASP ASN PRO LEU GLY PHE GLN ILE ALA LYS ARG THR SEQRES 14 B 186 ILE ILE LEU ASP GLN SER THR VAL LEU ALA ASN ASN LEU SEQRES 15 B 186 SER VAL PHE PHE HET FE2 A 701 1 HET FES A 700 4 HET BNL A 702 12 HET GOL A 705 6 HET GOL A 706 6 HET MES B 704 24 HETNAM FE2 FE (II) ION HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM BNL BIPHENYL HETNAM GOL GLYCEROL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FE2 FE 2+ FORMUL 4 FES FE2 S2 FORMUL 5 BNL C12 H10 FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 MES C6 H13 N O4 S FORMUL 9 HOH *640(H2 O) HELIX 1 1 THR A 20 ALA A 26 1 7 HELIX 2 2 ARG A 38 ALA A 41 5 4 HELIX 3 3 ASP A 42 VAL A 53 1 12 HELIX 4 4 THR A 65 ILE A 67 5 3 HELIX 5 5 PHE A 138 PHE A 143 1 6 HELIX 6 6 ASP A 154 TRP A 158 5 5 HELIX 7 7 ASP A 182 LEU A 187 1 6 HELIX 8 8 ALA A 190 ASP A 199 1 10 HELIX 9 9 ASN A 219 ASP A 230 1 12 HELIX 10 10 HIS A 239 GLY A 246 1 8 HELIX 11 11 SER A 281 GLN A 298 1 18 HELIX 12 12 GLY A 299 VAL A 309 1 11 HELIX 13 13 PRO A 313 LEU A 315 5 3 HELIX 14 14 PRO A 361 PHE A 376 1 16 HELIX 15 15 PHE A 382 MET A 397 1 16 HELIX 16 16 LYS A 401 SER A 404 5 4 HELIX 17 17 GLU A 433 GLU A 449 1 17 HELIX 18 18 SER A 451 LYS A 456 1 6 HELIX 19 19 SER B 18 HIS B 38 1 21 HELIX 20 20 ALA B 40 ALA B 46 1 7 HELIX 21 21 THR B 63 GLU B 70 5 8 HELIX 22 22 THR B 83 THR B 95 1 13 HELIX 23 23 ASN B 99 ASP B 103 5 5 SHEET 1 A 3 VAL A 28 ASP A 29 0 SHEET 2 A 3 LYS A 34 ASP A 36 -1 O LYS A 34 N ASP A 29 SHEET 3 A 3 SER A 406 CYS A 408 -1 O LEU A 407 N LEU A 35 SHEET 1 B 7 LEU A 59 HIS A 63 0 SHEET 2 B 7 LEU A 171 ASN A 175 -1 O VAL A 172 N GLY A 62 SHEET 3 B 7 GLN A 162 TYR A 168 -1 N ARG A 164 O ASN A 175 SHEET 4 B 7 ILE A 93 LEU A 97 -1 N VAL A 95 O ALA A 163 SHEET 5 B 7 ASP A 81 ARG A 87 -1 N ILE A 84 O PHE A 96 SHEET 6 B 7 ASP A 72 MET A 78 -1 N LEU A 74 O MET A 85 SHEET 7 B 7 GLY A 112 ASN A 114 -1 O GLY A 113 N TYR A 73 SHEET 1 C 3 ALA A 117 THR A 119 0 SHEET 2 C 3 ALA A 126 ASP A 128 -1 O TYR A 127 N PHE A 118 SHEET 3 C 3 LEU A 133 ASN A 135 -1 O ASN A 135 N ALA A 126 SHEET 1 D 3 THR A 205 ALA A 207 0 SHEET 2 D 3 VAL A 348 ASP A 357 -1 O VAL A 356 N GLU A 206 SHEET 3 D 3 GLN A 212 ILE A 216 -1 N GLN A 212 O ALA A 352 SHEET 1 E 8 THR A 205 ALA A 207 0 SHEET 2 E 8 VAL A 348 ASP A 357 -1 O VAL A 356 N GLU A 206 SHEET 3 E 8 THR A 336 PRO A 342 -1 N HIS A 341 O GLU A 349 SHEET 4 E 8 CYS A 328 PHE A 330 -1 N SER A 329 O ARG A 338 SHEET 5 E 8 MET A 317 VAL A 324 -1 N VAL A 324 O CYS A 328 SHEET 6 E 8 GLY A 273 ILE A 278 -1 N PHE A 277 O PHE A 318 SHEET 7 E 8 GLY A 262 ARG A 266 -1 N PHE A 265 O ALA A 274 SHEET 8 E 8 LYS A 426 TYR A 429 -1 O LYS A 426 N ARG A 266 SHEET 1 F 6 ALA B 78 ASP B 82 0 SHEET 2 F 6 LEU B 48 PRO B 57 -1 N TYR B 54 O ASP B 82 SHEET 3 F 6 PHE B 163 LEU B 172 1 O ARG B 168 N TRP B 55 SHEET 4 F 6 GLN B 142 ILE B 156 -1 N GLU B 149 O ILE B 171 SHEET 5 F 6 THR B 125 ARG B 138 -1 N ARG B 136 O ASP B 144 SHEET 6 F 6 ARG B 107 GLU B 119 -1 N ARG B 107 O SER B 137 LINK SG CYS A 100 FE1 FES A 700 1555 1555 2.33 LINK ND1 HIS A 102 FE2 FES A 700 1555 1555 2.12 LINK SG CYS A 120 FE1 FES A 700 1555 1555 2.21 LINK ND1 HIS A 123 FE2 FES A 700 1555 1555 2.14 LINK NE2 HIS A 233 FE FE2 A 701 1555 1555 2.11 LINK NE2 HIS A 239 FE FE2 A 701 1555 1555 2.13 LINK OD1 ASP A 386 FE FE2 A 701 1555 1555 2.23 LINK OD2 ASP A 386 FE FE2 A 701 1555 1555 2.46 LINK O HOH A 458 FE FE2 A 701 1555 1555 1.93 CISPEP 1 PHE A 325 PRO A 326 0 0.15 CISPEP 2 ASP B 103 PRO B 104 0 1.53 SITE 1 AC1 5 GLN A 226 HIS A 233 HIS A 239 ASP A 386 SITE 2 AC1 5 HOH A 458 SITE 1 AC2 6 CYS A 100 HIS A 102 ARG A 103 CYS A 120 SITE 2 AC2 6 HIS A 123 TRP A 125 SITE 1 AC3 7 GLN A 226 PHE A 227 ASP A 230 HIS A 233 SITE 2 AC3 7 GLY A 319 HIS A 321 LEU A 331 SITE 1 AC4 8 LEU A 74 ASP A 111 GLY A 112 HOH A 661 SITE 2 AC4 8 GOL A 706 HOH A 737 HOH A 756 ARG B 62 SITE 1 AC5 6 HIS A 66 PRO A 68 LYS A 69 ASP A 72 SITE 2 AC5 6 GOL A 705 HOH A 818 SITE 1 AC6 7 ASN A 279 HOH A 819 ARG B 118 MET B 120 SITE 2 AC6 7 ASP B 121 HOH B 515 HOH B 617 CRYST1 136.355 136.355 107.155 90.00 90.00 120.00 H 3 9 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 0.007334 0.004234 0.000000 0.00000 SCALE2 0.000000 0.008468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009332 0.00000