10 20 30 40 50 60 70 80 1KND - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 18-DEC-01 1KND
TITLE CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE COMPLEXED TITLE 2 WITH CATECHOL UNDER ANAEROBIC CONDITION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE, DHBD; COMPND 5 EC: 1.13.11.39; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA XENOVORANS; SOURCE 3 ORGANISM_TAXID: 266265; SOURCE 4 STRAIN: LB400; SOURCE 5 GENE: BPHC; SOURCE 6 EXPRESSION_SYSTEM: BURKHOLDERIA CEPACIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 292; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLEBD4; SOURCE 10 OTHER_DETAILS: HYPEREXPRESSED IN THE PARENT STRAIN (THIS ORGANISM SOURCE 11 HAS BEEN RECLASSIFIED. PRIOR PUBLICATIONS MAY REFER TO THIS SOURCE SOURCE 12 AS PSEUDOMONAS SP. STRAIN LB400.)
KEYWDS DIOXYGENASE, 2,3-DIHYDROXYBIPHENYL, CATECHOL, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.HAN,J.T.BOLIN
REVDAT 3 13-JUL-11 1KND 1 VERSN REVDAT 2 24-FEB-09 1KND 1 VERSN REVDAT 1 27-MAR-02 1KND 0
JRNL AUTH F.H.VAILLANCOURT,S.HAN,P.D.FORTIN,J.T.BOLIN,L.D.ELTIS JRNL TITL MOLECULAR BASIS FOR THE STABILIZATION AND INHIBITION OF 2, JRNL TITL 2 3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE BY T-BUTANOL. JRNL REF J.BIOL.CHEM. V. 273 34887 1998 JRNL REFN ISSN 0021-9258 JRNL PMID 9857017 JRNL DOI 10.1074/JBC.273.52.34887
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.HAN,L.D.ELTIS,K.N.TIMMIS,S.W.MUCHMORE,J.T.BOLIN REMARK 1 TITL CRYSTAL STRUCTURE OF THE BIPHENYL-CLEAVING EXTRADIOL REMARK 1 TITL 2 DIOXYGENASE FROM A PCB-DEGRADING PSEUDOMONAD. REMARK 1 REF SCIENCE V. 270 976 1995 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.T.BOLIN,L.D.ELTIS REMARK 1 TITL 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE. REMARK 1 REF HANDBOOK OF METALLOPROTEINS 632 2001 REMARK 1 PUBL JOHN WILEY AND SONS REMARK 1 REFN
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 30189 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 SET) : 0.164 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1797 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2292 REMARK 3 BIN FREE R VALUE : 0.2996 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 44 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2216 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.20 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.000 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.900 ; 1.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 1.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ALL FE-PROTEIN BOND DISTANCES WERE HARMONICALLY RESTRAINED TO AN REMARK 3 EQUILIBRIUM DISTANCE OF 2.2 ANGSTROMS USING A WEAK FORCE CONSTANT REMARK 3 OF 10 KCAL/(MOLE X ANGSTROM-SQUARED). BOND LENGTH, BOND ANGLE, AND REMARK 3 PLANARITY RESTRAINTS SIMILAR TO THOSE USED FOR AROMATIC SIDE CHAINS REMARK 3 WERE APPLIED TO HET GROUP CAQ (CATECHOL). FE-CAQ AND FE-WATER BOND REMARK 3 DISTANCES WERE NOT RESTRAINED. REMARK 3 REMARK 3 THE REFINED MODEL INCLUDES TWO MUTALLY EXCLUSIVE STRUCTURES IN THE REMARK 3 VICINITY OF THE ACTIVE SITE. STRUCTURE ONE (LABELED WITH ALTERNATE REMARK 3 CONFORMATION MARKER A) INCLUDES THE SUBSTRATE CATECHOL (CAQ 301) REMARK 3 AND WATERS 9001 AND 9002 AT 50% OCCUPANCY. ATOMS O3 AND O4 OF CAQ REMARK 3 301 AND WATER 9001 ARE COORDINATED TO FE2 500. STRUCTURE TWO REMARK 3 (LABELED WITH ALTERNATE CONFORMATION MARKER B) INCLUDES ONE REMARK 3 MOLECULE OF T-BUTANOL (TBU 600) AND WATERS 3001, 3012, AND 4014 AT REMARK 3 50% OCCUPANCY, AND IS EQUIVALENT TO THE SUBSTRATE-FREE STRUCTURE REMARK 3 WHERE WATERS 3001 AND 3012 ARE COORDINATED TO FE2 500.
REMARK 4 REMARK 4 1KND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-01. REMARK 100 THE RCSB ID CODE IS RCSB015139.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-95 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 44.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.100 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: 1HAN REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, T-BUTANOL, CATECHOL, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 278K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 61.40000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 61.40000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 55.30000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 61.40000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 61.40000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 55.30000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 61.40000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 61.40000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 55.30000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 61.40000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 61.40000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 55.30000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 61.40000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 61.40000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 55.30000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 61.40000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 61.40000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 55.30000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 61.40000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 61.40000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 55.30000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 61.40000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 61.40000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 55.30000 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 ASSEMBLY IS HOMO-OCTAMER GENERATED BY REMARK 300 CRYSTALLOGRAPHIC SYMMETRY
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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 26350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 77950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -157.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 110.60000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 110.60000 REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 110.60000 REMARK 350 BIOMT1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 110.60000
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 ASP A 290 REMARK 465 LYS A 291 REMARK 465 ALA A 292 REMARK 465 ALA A 293 REMARK 465 ALA A 294 REMARK 465 ARG A 295 REMARK 465 ASN A 296 REMARK 465 LYS A 297 REMARK 465 ALA A 298
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 44 -152.38 -158.04 REMARK 500 PHE A 106 -173.31 -173.61 REMARK 500 LYS A 126 78.88 -119.76 REMARK 500 ALA A 133 96.97 -68.81 REMARK 500 THR A 139 -100.62 -129.55 REMARK 500 MET A 177 77.25 -113.24 REMARK 500 ASN A 191 -161.51 -164.61 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 FE2 A 500 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 260 OE2 REMARK 620 2 HIS A 146 NE2 105.4 REMARK 620 3 HIS A 210 NE2 88.3 100.6 REMARK 620 4 HOH A3001 O 80.1 95.8 162.0 REMARK 620 5 HOH A3012 O 154.0 94.4 104.8 81.3 REMARK 620 6 HOH A9001 O 171.9 80.0 84.7 105.8 27.4 REMARK 620 7 CAQ A 301 O3 104.9 103.9 147.7 29.5 52.9 79.3 REMARK 620 8 CAQ A 301 O4 100.9 153.5 77.2 91.5 61.6 73.6 71.5 REMARK 620 N 1 2 3 4 5 6 7
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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAQ A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBU A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBU A 600
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HAN RELATED DB: PDB REMARK 900 1HAN IS THE SAME PROTEIN WITHOUT SUBSTRATE. REMARK 900 RELATED ID: 1KMY RELATED DB: PDB REMARK 900 1KMY IS THE CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2- REMARK 900 DIOXYGENASE COMPLEXED WITH 2,3-DIHYDROXYBIPHENYL UNDER REMARK 900 ANAEROBIC CONDITION. REMARK 900 RELATED ID: 1KNF RELATED DB: PDB REMARK 900 1KNF IS THE CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2- REMARK 900 DIOXYGENASE COMPLEXED WITH 3-METHYL CATECHOL UNDER REMARK 900 ANAEROBIC CONDITION.
DBREF 1KND A 2 298 UNP P47228 BPHC_BURCE 1 297
SEQRES 1 A 297 SER ILE ARG SER LEU GLY TYR MET GLY PHE ALA VAL SER SEQRES 2 A 297 ASP VAL ALA ALA TRP ARG SER PHE LEU THR GLN LYS LEU SEQRES 3 A 297 GLY LEU MET GLU ALA GLY THR THR ASP ASN GLY ASP LEU SEQRES 4 A 297 PHE ARG ILE ASP SER ARG ALA TRP ARG ILE ALA VAL GLN SEQRES 5 A 297 GLN GLY GLU VAL ASP ASP LEU ALA PHE ALA GLY TYR GLU SEQRES 6 A 297 VAL ALA ASP ALA ALA GLY LEU ALA GLN MET ALA ASP LYS SEQRES 7 A 297 LEU LYS GLN ALA GLY ILE ALA VAL THR THR GLY ASP ALA SEQRES 8 A 297 SER LEU ALA ARG ARG ARG GLY VAL THR GLY LEU ILE THR SEQRES 9 A 297 PHE ALA ASP PRO PHE GLY LEU PRO LEU GLU ILE TYR TYR SEQRES 10 A 297 GLY ALA SER GLU VAL PHE GLU LYS PRO PHE LEU PRO GLY SEQRES 11 A 297 ALA ALA VAL SER GLY PHE LEU THR GLY GLU GLN GLY LEU SEQRES 12 A 297 GLY HIS PHE VAL ARG CYS VAL PRO ASP SER ASP LYS ALA SEQRES 13 A 297 LEU ALA PHE TYR THR ASP VAL LEU GLY PHE GLN LEU SER SEQRES 14 A 297 ASP VAL ILE ASP MET LYS MET GLY PRO ASP VAL THR VAL SEQRES 15 A 297 PRO ALA TYR PHE LEU HIS CYS ASN GLU ARG HIS HIS THR SEQRES 16 A 297 LEU ALA ILE ALA ALA PHE PRO LEU PRO LYS ARG ILE HIS SEQRES 17 A 297 HIS PHE MET LEU GLU VAL ALA SER LEU ASP ASP VAL GLY SEQRES 18 A 297 PHE ALA PHE ASP ARG VAL ASP ALA ASP GLY LEU ILE THR SEQRES 19 A 297 SER THR LEU GLY ARG HIS THR ASN ASP HIS MET VAL SER SEQRES 20 A 297 PHE TYR ALA SER THR PRO SER GLY VAL GLU VAL GLU TYR SEQRES 21 A 297 GLY TRP SER ALA ARG THR VAL ASP ARG SER TRP VAL VAL SEQRES 22 A 297 VAL ARG HIS ASP SER PRO SER MET TRP GLY HIS LYS SER SEQRES 23 A 297 VAL ARG ASP LYS ALA ALA ALA ARG ASN LYS ALA
HET FE2 A 500 1 HET FE2 A 501 1 HET CAQ A 301 8 HET TBU A 601 5 HET TBU A 600 5
HETNAM FE2 FE (II) ION HETNAM CAQ CATECHOL HETNAM TBU TERTIARY-BUTYL ALCOHOL
HETSYN CAQ 1,2-DIHYDROXYBENZENE HETSYN TBU 2-METHYL-2-PROPANOL
FORMUL 2 FE2 2(FE 2+) FORMUL 4 CAQ C6 H6 O2 FORMUL 5 TBU 2(C4 H10 O) FORMUL 7 HOH *121(H2 O)
HELIX 1 1 ASP A 15 LYS A 26 1 12 HELIX 2 2 ASP A 69 ALA A 83 1 15 HELIX 3 3 ASP A 91 GLY A 99 1 9 HELIX 4 4 THR A 139 GLY A 143 5 5 HELIX 5 5 ASP A 153 VAL A 164 1 12 HELIX 6 6 SER A 217 ALA A 230 1 14
SHEET 1 A 8 MET A 30 THR A 35 0 SHEET 2 A 8 GLY A 38 ARG A 42 -1 O ARG A 42 N MET A 30 SHEET 3 A 8 ILE A 50 GLN A 54 -1 O VAL A 52 N ASP A 39 SHEET 4 A 8 SER A 5 VAL A 13 1 N VAL A 13 O GLN A 53 SHEET 5 A 8 ASP A 59 GLU A 66 -1 O ALA A 61 N GLY A 10 SHEET 6 A 8 PRO A 113 TYR A 118 1 O GLU A 115 N TYR A 65 SHEET 7 A 8 GLY A 102 ALA A 107 -1 N PHE A 106 O LEU A 114 SHEET 8 A 8 THR A 88 THR A 89 -1 N THR A 88 O THR A 105 SHEET 1 B10 VAL A 275 HIS A 277 0 SHEET 2 B10 GLN A 168 LYS A 176 1 N VAL A 172 O HIS A 277 SHEET 3 B10 THR A 182 HIS A 189 -1 O HIS A 189 N GLN A 168 SHEET 4 B10 LEU A 197 ALA A 200 -1 O LEU A 197 N LEU A 188 SHEET 5 B10 HIS A 146 CYS A 150 1 N ARG A 149 O ALA A 198 SHEET 6 B10 ILE A 208 GLU A 214 -1 O MET A 212 N HIS A 146 SHEET 7 B10 GLU A 258 TRP A 263 1 O GLU A 260 N PHE A 211 SHEET 8 B10 VAL A 247 SER A 252 -1 N ALA A 251 O VAL A 259 SHEET 9 B10 ILE A 234 HIS A 241 -1 N GLY A 239 O SER A 248 SHEET 10 B10 SER A 281 GLY A 284 -1 O MET A 282 N ARG A 240
LINK OE2 GLU A 260 FE FE2 A 500 1555 1555 1.97 LINK NE2 HIS A 146 FE FE2 A 500 1555 1555 2.10 LINK NE2 HIS A 210 FE FE2 A 500 1555 1555 2.27 LINK O BHOH A3001 FE FE2 A 500 1555 1555 2.49 LINK O BHOH A3012 FE FE2 A 500 1555 1555 2.11 LINK O AHOH A9001 FE FE2 A 500 1555 1555 2.28 LINK O3 ACAQ A 301 FE FE2 A 500 1555 1555 2.33 LINK O4 ACAQ A 301 FE FE2 A 500 1555 1555 2.36 LINK FE FE2 A 501 NE2 HIS A 189 1555 1555 2.51
SITE 1 AC1 7 HIS A 146 HIS A 210 GLU A 260 CAQ A 301 SITE 2 AC1 7 HOH A3001 HOH A3012 HOH A9001 SITE 1 AC2 1 HIS A 189 SITE 1 AC3 14 HIS A 146 PHE A 187 HIS A 195 HIS A 210 SITE 2 AC3 14 HIS A 241 ASN A 243 ASP A 244 TYR A 250 SITE 3 AC3 14 GLU A 260 FE2 A 500 HOH A3001 HOH A3012 SITE 4 AC3 14 HOH A9001 HOH A9002 SITE 1 AC4 4 SER A 236 TYR A 250 ARG A 289 TBU A 600 SITE 1 AC5 4 PHE A 202 TYR A 250 PRO A 280 TBU A 601
CRYST1 122.800 122.800 110.600 90.00 90.00 90.00 I 4 2 2 16
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 0.008143 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008143 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009042 0.00000