HEADER OXIDOREDUCTASE 23-JUL-11 3ZV5 TITLE CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE TITLE 2 (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 COMPLEX WITH CO-ENZYME TITLE 3 NAD AND PRODUCT 2,3-DIHYDROXYBIPHENYL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 2,3-DIHYDRO-2,3-DIHYDROXYBIPHENYL DEHYDROGENASE, 2,3- COMPND 5 DIHYDROXY-4-PHENYLHEXA-4,6-DIENE DEHYDROGENASE, B2\,3D, BIPHENYL-2,3- COMPND 6 DIHYDRO-2,3-DIOL DEHYDROGENASE, BIPHENYL-CIS-DIOL DEHYDROGENASE; COMPND 7 EC: 1.3.1.56; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PANDORAEA PNOMENUSA; SOURCE 3 ORGANISM_TAXID: 93220; SOURCE 4 STRAIN: B-356; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET14B KEYWDS OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/OXIDOREDUCTASE, SDR, KEYWDS 2 COMAMONAS TESTOSTERONI EXPDTA X-RAY DIFFRACTION AUTHOR S.DHINDWAL,D.N.PATIL,P.KUMAR REVDAT 3 20-DEC-23 3ZV5 1 REMARK REVDAT 2 26-OCT-11 3ZV5 1 JRNL REVDAT 1 31-AUG-11 3ZV5 0 JRNL AUTH S.DHINDWAL,D.N.PATIL,M.MOHAMMADI,M.SYLVESTRE,S.TOMAR,P.KUMAR JRNL TITL BIOCHEMICAL STUDIES AND LIGAND-BOUND STRUCTURES OF BIPHENYL JRNL TITL 2 DEHYDROGENASE FROM PANDORAEA PNOMENUSA STRAIN B-356 REVEAL A JRNL TITL 3 BASIS FOR BROAD SPECIFICITY OF THE ENZYME. JRNL REF J.BIOL.CHEM. V. 286 37011 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21880718 JRNL DOI 10.1074/JBC.M111.291013 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.N.PATIL,S.TOMAR,M.SYLVESTRE,P.KUMAR REMARK 1 TITL EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY REMARK 1 TITL 2 CRYSTALLOGRAPHIC STUDIES OF REMARK 1 TITL 3 CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM REMARK 1 TITL 4 PANDORAEA PNOMENUSA B-356. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 66 1517 2010 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 21045310 REMARK 1 DOI 10.1107/S1744309110036894 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 18141 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 982 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1306 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3978 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.68000 REMARK 3 B22 (A**2) : 1.68000 REMARK 3 B33 (A**2) : -3.36000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.935 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.319 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.232 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.430 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4160 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5659 ; 1.776 ; 2.010 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 540 ; 6.497 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 156 ;38.950 ;23.205 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 631 ;19.538 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;20.136 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 651 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3134 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2177 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2795 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 215 ; 0.169 ; 0.200 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): 120 ; 0.241 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.163 ; 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): 2747 ; 0.619 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4238 ; 1.014 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1639 ; 1.803 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1421 ; 2.744 ; 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 : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 185 REMARK 3 ORIGIN FOR THE GROUP (A): 13.6784 -16.9687 -9.6446 REMARK 3 T TENSOR REMARK 3 T11: -0.0572 T22: -0.0228 REMARK 3 T33: -0.1228 T12: 0.0678 REMARK 3 T13: -0.0073 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.2157 L22: 0.9577 REMARK 3 L33: 1.3578 L12: 0.0400 REMARK 3 L13: -0.5678 L23: 0.3356 REMARK 3 S TENSOR REMARK 3 S11: 0.0150 S12: 0.1140 S13: -0.0956 REMARK 3 S21: -0.1198 S22: 0.0015 S23: -0.0515 REMARK 3 S31: 0.2447 S32: 0.2854 S33: -0.0165 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 186 A 226 REMARK 3 ORIGIN FOR THE GROUP (A): -2.4172 -25.8341 -8.2018 REMARK 3 T TENSOR REMARK 3 T11: 0.0819 T22: 0.0171 REMARK 3 T33: 0.1234 T12: 0.0373 REMARK 3 T13: 0.0285 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 2.5728 L22: 1.9467 REMARK 3 L33: 3.5661 L12: -1.8618 REMARK 3 L13: 2.4344 L23: -0.8917 REMARK 3 S TENSOR REMARK 3 S11: 0.2874 S12: 0.0002 S13: -0.7881 REMARK 3 S21: -0.1028 S22: 0.0665 S23: 0.4657 REMARK 3 S31: 0.4273 S32: -0.0873 S33: -0.3539 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 227 A 275 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2291 -8.4448 -14.2014 REMARK 3 T TENSOR REMARK 3 T11: -0.0346 T22: -0.1074 REMARK 3 T33: -0.1068 T12: 0.0316 REMARK 3 T13: -0.0268 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 2.6824 L22: 1.9792 REMARK 3 L33: 1.8151 L12: 0.6842 REMARK 3 L13: -0.1840 L23: -0.0171 REMARK 3 S TENSOR REMARK 3 S11: -0.0436 S12: 0.2489 S13: 0.0615 REMARK 3 S21: -0.2504 S22: 0.0508 S23: 0.2186 REMARK 3 S31: 0.1917 S32: -0.1532 S33: -0.0071 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 185 REMARK 3 ORIGIN FOR THE GROUP (A): -10.6844 8.3899 -19.5160 REMARK 3 T TENSOR REMARK 3 T11: -0.0534 T22: -0.0944 REMARK 3 T33: -0.1261 T12: 0.0439 REMARK 3 T13: 0.0019 T23: 0.0305 REMARK 3 L TENSOR REMARK 3 L11: 1.3064 L22: 0.9363 REMARK 3 L33: 2.1947 L12: 0.3865 REMARK 3 L13: 0.4469 L23: 0.2464 REMARK 3 S TENSOR REMARK 3 S11: -0.0335 S12: 0.1339 S13: 0.0522 REMARK 3 S21: -0.2172 S22: 0.0133 S23: 0.0384 REMARK 3 S31: -0.2657 S32: -0.1336 S33: 0.0202 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 186 B 213 REMARK 3 ORIGIN FOR THE GROUP (A): 2.4993 20.7114 -13.3023 REMARK 3 T TENSOR REMARK 3 T11: 0.6005 T22: 0.2287 REMARK 3 T33: 0.4572 T12: 0.1090 REMARK 3 T13: 0.0992 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 2.0096 L22: 0.1686 REMARK 3 L33: 0.3374 L12: -0.5821 REMARK 3 L13: 0.8234 L23: -0.2385 REMARK 3 S TENSOR REMARK 3 S11: 0.1474 S12: -0.1641 S13: 1.9083 REMARK 3 S21: 0.5755 S22: 0.0833 S23: -0.4788 REMARK 3 S31: -0.7453 S32: 0.0164 S33: -0.2306 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 214 B 275 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4291 2.2016 -13.4106 REMARK 3 T TENSOR REMARK 3 T11: -0.0638 T22: -0.0795 REMARK 3 T33: -0.1307 T12: -0.0078 REMARK 3 T13: 0.0313 T23: 0.0107 REMARK 3 L TENSOR REMARK 3 L11: 2.4865 L22: 2.1318 REMARK 3 L33: 1.7189 L12: 0.2373 REMARK 3 L13: -0.2215 L23: -0.0935 REMARK 3 S TENSOR REMARK 3 S11: 0.0106 S12: 0.0590 S13: 0.1968 REMARK 3 S21: -0.0534 S22: -0.0132 S23: -0.1578 REMARK 3 S31: -0.2048 S32: 0.3211 S33: 0.0026 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 3ZV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1290049144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20162 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 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 : 12.10 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 69.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.290 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: PDB ENTRY 1BDB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM MALONATE, PEG3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 86.78350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.69700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.69700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 130.17525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.69700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.69700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.39175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.69700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.69700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 130.17525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.69700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.69700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.39175 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 86.78350 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 24100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -183.3 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ARG A 277 REMARK 465 GLU A 278 REMARK 465 GLY A 279 REMARK 465 GLN A 280 REMARK 465 GLU A 281 REMARK 465 LEU B 199 REMARK 465 SER B 200 REMARK 465 GLU B 201 REMARK 465 GLN B 202 REMARK 465 SER B 203 REMARK 465 ILE B 204 REMARK 465 SER B 205 REMARK 465 ARG B 277 REMARK 465 GLU B 278 REMARK 465 GLY B 279 REMARK 465 GLN B 280 REMARK 465 GLU B 281 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 276 CA C O CB CG OD1 ND2 REMARK 470 ASN B 276 CA C O CB CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 142 OK1 BPY A 1278 2.18 REMARK 500 NH1 ARG A 31 ND2 ASN A 52 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 45 CA - CB - CG ANGL. DEV. = 16.8 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 ILE A 84 79.70 -117.42 REMARK 500 ASN A 86 -24.60 -155.49 REMARK 500 ILE A 141 -126.51 -94.64 REMARK 500 SER A 142 160.27 170.16 REMARK 500 PHE A 146 -36.41 -137.05 REMARK 500 PRO A 148 -166.26 -65.99 REMARK 500 ASN A 149 8.80 56.77 REMARK 500 THR A 189 -154.34 -119.48 REMARK 500 ARG A 221 157.11 179.00 REMARK 500 ASN A 274 84.94 27.89 REMARK 500 ASN B 86 -21.01 -142.71 REMARK 500 ILE B 141 -120.70 -101.16 REMARK 500 SER B 142 155.58 167.27 REMARK 500 PHE B 146 -40.23 -137.32 REMARK 500 ASP B 190 49.23 -79.14 REMARK 500 SER B 196 -26.95 -32.61 REMARK 500 TYR B 251 50.73 -143.31 REMARK 500 ILE B 275 50.01 -94.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2007 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH B2008 DISTANCE = 6.93 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 1277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 1277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BPY A 1278 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y99 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3- REMARK 900 DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B -356 COMPLEX REMARK 900 WITH CO-ENZYME NAD REMARK 900 RELATED ID: 2Y93 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3- REMARK 900 DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B -356. REMARK 900 RELATED ID: 3ZV6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3- REMARK 900 DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B -356 COMPLEX REMARK 900 WITH CO-ENZYME NAD AND PRODUCT ANALOG 4,4'-DIHYDROXYBIPHENYL REMARK 900 RELATED ID: 3ZV4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3- REMARK 900 DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B -356 IN APO REMARK 900 FORM AT 1.8 ANGSTROM REMARK 900 RELATED ID: 3ZV3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3- REMARK 900 DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B -356 IN REMARK 900 INTERMEDIATE STATE OF SUBSTRATE BINDING LOOP DBREF 3ZV5 A 1 281 UNP Q46381 BPHB_COMTE 1 281 DBREF 3ZV5 B 1 281 UNP Q46381 BPHB_COMTE 1 281 SEQRES 1 A 281 MET LYS LEU THR GLY GLU VAL ALA LEU ILE THR GLY GLY SEQRES 2 A 281 ALA SER GLY LEU GLY ARG ALA LEU VAL ASP ARG PHE VAL SEQRES 3 A 281 ALA GLU GLY ALA ARG VAL ALA VAL LEU ASP LYS SER ALA SEQRES 4 A 281 GLU ARG LEU ARG GLU LEU GLU VAL ALA HIS GLY GLY ASN SEQRES 5 A 281 ALA VAL GLY VAL VAL GLY ASP VAL ARG SER LEU GLN ASP SEQRES 6 A 281 GLN LYS ARG ALA ALA GLU ARG CYS LEU ALA ALA PHE GLY SEQRES 7 A 281 LYS ILE ASP THR LEU ILE PRO ASN ALA GLY ILE TRP ASP SEQRES 8 A 281 TYR SER THR ALA LEU ALA ASP LEU PRO GLU ASP LYS ILE SEQRES 9 A 281 ASP ALA ALA PHE ASP ASP ILE PHE HIS VAL ASN VAL LYS SEQRES 10 A 281 GLY TYR ILE HIS ALA VAL LYS ALA CYS LEU PRO ALA LEU SEQRES 11 A 281 VAL SER SER ARG GLY SER VAL VAL PHE THR ILE SER ASN SEQRES 12 A 281 ALA GLY PHE TYR PRO ASN GLY GLY GLY PRO LEU TYR THR SEQRES 13 A 281 ALA THR LYS HIS ALA VAL VAL GLY LEU VAL ARG GLN MET SEQRES 14 A 281 ALA PHE GLU LEU ALA PRO HIS VAL ARG VAL ASN GLY VAL SEQRES 15 A 281 ALA PRO GLY GLY MET ASN THR ASP LEU ARG GLY PRO SER SEQRES 16 A 281 SER LEU GLY LEU SER GLU GLN SER ILE SER SER VAL PRO SEQRES 17 A 281 LEU ALA ASP MET LEU LYS SER VAL LEU PRO ILE GLY ARG SEQRES 18 A 281 MET PRO ALA LEU GLU GLU TYR THR GLY ALA TYR VAL PHE SEQRES 19 A 281 PHE ALA THR ARG GLY ASP SER LEU PRO ALA THR GLY ALA SEQRES 20 A 281 LEU LEU ASN TYR ASP GLY GLY MET GLY VAL ARG GLY PHE SEQRES 21 A 281 LEU THR ALA ALA GLY GLY ALA ASP LEU PRO GLU LYS LEU SEQRES 22 A 281 ASN ILE ASN ARG GLU GLY GLN GLU SEQRES 1 B 281 MET LYS LEU THR GLY GLU VAL ALA LEU ILE THR GLY GLY SEQRES 2 B 281 ALA SER GLY LEU GLY ARG ALA LEU VAL ASP ARG PHE VAL SEQRES 3 B 281 ALA GLU GLY ALA ARG VAL ALA VAL LEU ASP LYS SER ALA SEQRES 4 B 281 GLU ARG LEU ARG GLU LEU GLU VAL ALA HIS GLY GLY ASN SEQRES 5 B 281 ALA VAL GLY VAL VAL GLY ASP VAL ARG SER LEU GLN ASP SEQRES 6 B 281 GLN LYS ARG ALA ALA GLU ARG CYS LEU ALA ALA PHE GLY SEQRES 7 B 281 LYS ILE ASP THR LEU ILE PRO ASN ALA GLY ILE TRP ASP SEQRES 8 B 281 TYR SER THR ALA LEU ALA ASP LEU PRO GLU ASP LYS ILE SEQRES 9 B 281 ASP ALA ALA PHE ASP ASP ILE PHE HIS VAL ASN VAL LYS SEQRES 10 B 281 GLY TYR ILE HIS ALA VAL LYS ALA CYS LEU PRO ALA LEU SEQRES 11 B 281 VAL SER SER ARG GLY SER VAL VAL PHE THR ILE SER ASN SEQRES 12 B 281 ALA GLY PHE TYR PRO ASN GLY GLY GLY PRO LEU TYR THR SEQRES 13 B 281 ALA THR LYS HIS ALA VAL VAL GLY LEU VAL ARG GLN MET SEQRES 14 B 281 ALA PHE GLU LEU ALA PRO HIS VAL ARG VAL ASN GLY VAL SEQRES 15 B 281 ALA PRO GLY GLY MET ASN THR ASP LEU ARG GLY PRO SER SEQRES 16 B 281 SER LEU GLY LEU SER GLU GLN SER ILE SER SER VAL PRO SEQRES 17 B 281 LEU ALA ASP MET LEU LYS SER VAL LEU PRO ILE GLY ARG SEQRES 18 B 281 MET PRO ALA LEU GLU GLU TYR THR GLY ALA TYR VAL PHE SEQRES 19 B 281 PHE ALA THR ARG GLY ASP SER LEU PRO ALA THR GLY ALA SEQRES 20 B 281 LEU LEU ASN TYR ASP GLY GLY MET GLY VAL ARG GLY PHE SEQRES 21 B 281 LEU THR ALA ALA GLY GLY ALA ASP LEU PRO GLU LYS LEU SEQRES 22 B 281 ASN ILE ASN ARG GLU GLY GLN GLU HET NAD A1277 44 HET BPY A1278 14 HET NAD B1277 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM BPY BIPHENYL-2,3-DIOL FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 BPY C12 H10 O2 FORMUL 6 HOH *132(H2 O) HELIX 1 1 SER A 15 GLU A 28 1 14 HELIX 2 2 SER A 38 GLY A 50 1 13 HELIX 3 3 SER A 62 GLY A 78 1 17 HELIX 4 4 PRO A 100 VAL A 116 1 17 HELIX 5 5 VAL A 116 ARG A 134 1 19 HELIX 6 6 SER A 142 PHE A 146 5 5 HELIX 7 7 GLY A 152 ALA A 174 1 23 HELIX 8 8 PRO A 194 GLY A 198 5 5 HELIX 9 9 SER A 203 VAL A 207 5 5 HELIX 10 10 PRO A 208 LEU A 217 1 10 HELIX 11 11 ALA A 224 TYR A 228 5 5 HELIX 12 12 THR A 229 THR A 237 1 9 HELIX 13 13 THR A 237 LEU A 242 1 6 HELIX 14 14 GLY A 254 ARG A 258 5 5 HELIX 15 15 ASP A 268 LEU A 273 1 6 HELIX 16 16 SER B 15 GLU B 28 1 14 HELIX 17 17 SER B 38 HIS B 49 1 12 HELIX 18 18 SER B 62 GLY B 78 1 17 HELIX 19 19 ALA B 95 LEU B 99 5 5 HELIX 20 20 LYS B 103 VAL B 116 1 14 HELIX 21 21 VAL B 116 ARG B 134 1 19 HELIX 22 22 SER B 142 PHE B 146 5 5 HELIX 23 23 GLY B 152 ALA B 174 1 23 HELIX 24 24 LEU B 209 VAL B 216 5 8 HELIX 25 25 ALA B 224 TYR B 228 5 5 HELIX 26 26 THR B 229 THR B 237 1 9 HELIX 27 27 THR B 237 LEU B 242 1 6 HELIX 28 28 GLY B 254 ARG B 258 5 5 HELIX 29 29 ASP B 268 LEU B 273 1 6 SHEET 1 AA 7 ALA A 53 VAL A 57 0 SHEET 2 AA 7 ARG A 31 ASP A 36 1 O VAL A 32 N VAL A 54 SHEET 3 AA 7 VAL A 7 THR A 11 1 O ALA A 8 N ALA A 33 SHEET 4 AA 7 THR A 82 ILE A 84 1 O THR A 82 N LEU A 9 SHEET 5 AA 7 SER A 136 THR A 140 1 O SER A 136 N LEU A 83 SHEET 6 AA 7 ARG A 178 PRO A 184 1 O ARG A 178 N VAL A 137 SHEET 7 AA 7 LEU A 248 TYR A 251 1 O LEU A 249 N ALA A 183 SHEET 1 BA 7 ALA B 53 VAL B 57 0 SHEET 2 BA 7 ARG B 31 ASP B 36 1 O VAL B 32 N VAL B 54 SHEET 3 BA 7 VAL B 7 THR B 11 1 O ALA B 8 N ALA B 33 SHEET 4 BA 7 THR B 82 ILE B 84 1 O THR B 82 N LEU B 9 SHEET 5 BA 7 SER B 136 THR B 140 1 O SER B 136 N LEU B 83 SHEET 6 BA 7 ARG B 178 PRO B 184 1 O ARG B 178 N VAL B 137 SHEET 7 BA 7 LEU B 248 TYR B 251 1 O LEU B 249 N ALA B 183 CISPEP 1 ALA A 174 PRO A 175 0 1.88 CISPEP 2 ALA B 174 PRO B 175 0 2.54 SITE 1 AC1 28 GLY A 12 SER A 15 GLY A 16 LEU A 17 SITE 2 AC1 28 ASP A 36 LYS A 37 GLY A 58 ASP A 59 SITE 3 AC1 28 VAL A 60 ARG A 61 ASN A 86 ALA A 87 SITE 4 AC1 28 GLY A 88 TYR A 119 THR A 140 ILE A 141 SITE 5 AC1 28 SER A 142 TYR A 155 LYS A 159 PRO A 184 SITE 6 AC1 28 GLY A 185 GLY A 186 MET A 187 THR A 189 SITE 7 AC1 28 ASP A 190 LEU A 191 BPY A1278 HOH A2026 SITE 1 AC2 24 GLY B 12 SER B 15 GLY B 16 LEU B 17 SITE 2 AC2 24 ASP B 36 LYS B 37 GLY B 58 ASP B 59 SITE 3 AC2 24 VAL B 60 ASN B 86 TYR B 119 THR B 140 SITE 4 AC2 24 ILE B 141 SER B 142 TYR B 155 LYS B 159 SITE 5 AC2 24 PRO B 184 MET B 187 THR B 189 LEU B 191 SITE 6 AC2 24 HOH B2007 HOH B2022 HOH B2037 HOH B2060 SITE 1 AC3 7 TRP A 90 SER A 142 ASN A 143 GLY A 150 SITE 2 AC3 7 TYR A 155 ILE A 204 NAD A1277 CRYST1 75.394 75.394 173.567 90.00 90.00 90.00 P 43 21 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 0.013264 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013264 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005761 0.00000