HEADER OXIDOREDUCTASE 08-APR-09 3GZY TITLE CRYSTAL STRUCTURE OF THE BIPHENYL DIOXYGENASE FROM COMAMONAS TITLE 2 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 3 01-NOV-23 3GZY 1 REMARK LINK REVDAT 2 06-FEB-13 3GZY 1 JRNL VERSN REVDAT 1 05-MAY-10 3GZY 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. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.118 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 91600 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.114 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 82604 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 : 17 REMARK 3 SOLVENT ATOMS : 580 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 5520.4 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 12 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 22850 REMARK 3 NUMBER OF RESTRAINTS : 21403 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.052 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.061 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.018 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.064 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3GZY 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_1000052517. 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 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 : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91600 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.19400 REMARK 200 R SYM FOR SHELL (I) : 0.19400 REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: PDB ENTRY 1NDO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-15% PEG 4000, 100MM MES, 10-15% 2 REMARK 280 -PROPANOL, SODIUM CHLORIDE, PH 6.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K, PH 6.00 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 68.11650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.32708 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.41233 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 68.11650 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 39.32708 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.41233 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 68.11650 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 39.32708 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.41233 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 78.65416 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 70.82467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 78.65416 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 70.82467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 78.65416 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 70.82467 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: 32390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 57550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -194.0 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 136.23300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 68.11650 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 117.98124 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 208 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 248 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 351 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 419 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 580 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 GLU A 51 CD OE1 OE2 REMARK 480 LYS A 69 CD CE NZ REMARK 480 LYS A 89 CE NZ REMARK 480 LYS A 116 CD CE NZ REMARK 480 LYS A 140 CE NZ REMARK 480 LYS A 184 CE NZ REMARK 480 ILE A 283 CG2 CD1 REMARK 480 LYS A 403 CE NZ REMARK 480 LYS A 456 NZ REMARK 480 ILE B 2 CD1 REMARK 480 LYS B 15 CD CE NZ REMARK 480 ARG B 65 CD NE CZ NH1 NH2 REMARK 480 ASP B 158 CG OD1 OD2 REMARK 480 LYS B 167 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY A 62 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 101 CG - CD - NE ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG A 106 CD - NE - CZ ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG A 106 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ASP A 111 CB - CG - OD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP A 128 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 PHE A 227 CG - CD2 - CE2 ANGL. DEV. = 6.9 DEGREES REMARK 500 CYS A 228 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP A 276 CH2 - CZ2 - CE2 ANGL. DEV. = 6.7 DEGREES REMARK 500 PHE A 330 CB - CG - CD2 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 338 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 338 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 TRP A 340 CH2 - CZ2 - CE2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 343 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 GLU A 349 O - C - N ANGL. DEV. = 15.3 DEGREES REMARK 500 ARG A 369 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP A 386 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 TYR A 429 CB - CG - CD1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 31 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASP B 37 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 TYR B 54 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 59 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 59 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 90 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 107 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 109 CD - NE - CZ ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG B 109 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 PHE B 132 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 PHE B 132 CB - CG - CD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 141 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 VAL B 143 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 ASP B 152 CB - CG - OD2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG B 155 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 168 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 THR B 169 O - C - N ANGL. DEV. = 9.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 56 19.15 -146.36 REMARK 500 THR A 76 -148.75 -153.39 REMARK 500 GLN A 91 -1.24 75.27 REMARK 500 ASP A 145 -73.33 -94.70 REMARK 500 LYS A 169 57.31 36.61 REMARK 500 SER A 188 -133.38 56.77 REMARK 500 SER A 229 -3.63 -147.08 REMARK 500 THR A 236 -104.28 -119.34 REMARK 500 THR A 375 -57.72 -120.59 REMARK 500 ASP B 81 89.15 -162.98 REMARK 500 LEU B 139 -138.92 49.14 REMARK 500 SER B 175 -77.57 -99.55 REMARK 500 SER B 183 24.43 -75.73 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 105.1 REMARK 620 3 FES A 700 S2 113.9 106.1 REMARK 620 4 CYS A 120 SG 109.2 111.5 110.8 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 110.4 REMARK 620 3 FES A 700 S2 118.1 109.1 REMARK 620 4 HIS A 123 ND1 83.5 115.7 118.1 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 95.3 REMARK 620 3 ASP A 386 OD1 88.6 93.4 REMARK 620 4 ASP A 386 OD2 143.6 98.6 57.2 REMARK 620 5 HOH A 514 O 107.9 102.1 156.0 101.8 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 MES B 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GZX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BIPHENYL DIOXYGENASE IN COMPLEX WITH REMARK 900 BIPHENYL FROM COMAMONAS 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 3GZY A 1 457 UNP Q46372 BPHA_COMTE 1 457 DBREF 3GZY 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 MES B 702 12 HETNAM FE2 FE (II) ION HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 3 FE2 FE 2+ FORMUL 4 FES FE2 S2 FORMUL 5 MES C6 H13 N O4 S FORMUL 6 HOH *580(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 MET A 231 THR A 236 1 6 HELIX 11 11 HIS A 239 LEU A 247 1 9 HELIX 12 12 ASP A 252 ILE A 256 5 5 HELIX 13 13 SER A 281 GLN A 298 1 18 HELIX 14 14 GLY A 299 VAL A 309 1 11 HELIX 15 15 PRO A 313 LEU A 315 5 3 HELIX 16 16 PRO A 361 PHE A 376 1 16 HELIX 17 17 PHE A 382 MET A 397 1 16 HELIX 18 18 LYS A 401 SER A 404 5 4 HELIX 19 19 GLU A 433 GLU A 449 1 17 HELIX 20 20 SER A 451 LYS A 456 1 6 HELIX 21 21 SER B 18 HIS B 38 1 21 HELIX 22 22 ALA B 40 ALA B 46 1 7 HELIX 23 23 THR B 63 GLU B 70 5 8 HELIX 24 24 THR B 83 THR B 95 1 13 HELIX 25 25 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 LEU A 61 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 VAL A 86 O LYS A 94 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 PHE A 118 THR A 119 0 SHEET 2 C 3 ALA A 126 TYR A 127 -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 ILE A 337 O PHE A 353 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 ALA A 428 N GLN A 264 SHEET 1 F 6 PHE B 80 ASP B 82 0 SHEET 2 F 6 LEU B 48 MET B 56 -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 HIS B 53 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 LEU B 134 O PHE B 146 SHEET 6 F 6 ARG B 107 GLU B 119 -1 N SER B 113 O ALA B 131 LINK SG CYS A 100 FE1 FES A 700 1555 1555 2.37 LINK ND1 HIS A 102 FE2 FES A 700 1555 1555 2.34 LINK SG CYS A 120 FE1 FES A 700 1555 1555 2.30 LINK ND1 HIS A 123 FE2 FES A 700 1555 1555 2.17 LINK NE2 HIS A 233 FE FE2 A 701 1555 1555 2.31 LINK NE2 HIS A 239 FE FE2 A 701 1555 1555 2.05 LINK OD1 ASP A 386 FE FE2 A 701 1555 1555 1.97 LINK OD2 ASP A 386 FE FE2 A 701 1555 1555 2.38 LINK O HOH A 514 FE FE2 A 701 1555 1555 2.03 CISPEP 1 PHE A 325 PRO A 326 0 -2.86 CISPEP 2 ASP B 103 PRO B 104 0 6.12 SITE 1 AC1 5 GLN A 226 HIS A 233 HIS A 239 ASP A 386 SITE 2 AC1 5 HOH A 514 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 8 ASN A 279 HOH A 641 HOH A 797 HOH A 825 SITE 2 AC3 8 ARG B 118 MET B 120 ASP B 121 HOH B 271 CRYST1 136.233 136.233 106.237 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 0.007340 0.004238 0.000000 0.00000 SCALE2 0.000000 0.008476 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009413 0.00000