HEADER OXIDOREDUCTASE 23-JUL-11 3ZV6 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 ANALOG 4,4'-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: COMAMONAS TESTOSTERONI; SOURCE 3 ORGANISM_TAXID: 285; 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 EXPDTA X-RAY DIFFRACTION AUTHOR S.DHINDWAL,D.N.PATIL,P.KUMAR REVDAT 3 20-DEC-23 3ZV6 1 REMARK REVDAT 2 26-OCT-11 3ZV6 1 JRNL REVDAT 1 31-AUG-11 3ZV6 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. 2.14 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 28211 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1509 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) : 2.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1971 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3976 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.24000 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): 0.253 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.885 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4169 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2758 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5672 ; 1.511 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6659 ; 1.052 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 542 ; 6.261 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;39.010 ;23.185 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 632 ;16.238 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;19.361 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 652 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4683 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 837 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 935 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3135 ; 0.199 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2044 ; 0.175 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2149 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 156 ; 0.145 ; 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): 36 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 103 ; 0.288 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.182 ; 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): 3399 ; 0.713 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1127 ; 0.153 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4240 ; 0.904 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1753 ; 1.639 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1431 ; 2.350 ; 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): 15.4150 14.5100 34.3361 REMARK 3 T TENSOR REMARK 3 T11: -0.1032 T22: -0.1031 REMARK 3 T33: -0.0956 T12: -0.0962 REMARK 3 T13: 0.0299 T23: 0.0265 REMARK 3 L TENSOR REMARK 3 L11: 1.1163 L22: 1.1865 REMARK 3 L33: 1.9252 L12: 0.2213 REMARK 3 L13: -0.4921 L23: -0.3805 REMARK 3 S TENSOR REMARK 3 S11: -0.0065 S12: 0.1291 S13: 0.1330 REMARK 3 S21: -0.1387 S22: 0.0057 S23: -0.1530 REMARK 3 S31: -0.2039 S32: 0.2840 S33: 0.0008 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): 24.4337 -1.5130 36.2585 REMARK 3 T TENSOR REMARK 3 T11: 0.0534 T22: 0.2453 REMARK 3 T33: 0.2968 T12: 0.0104 REMARK 3 T13: 0.0825 T23: 0.0465 REMARK 3 L TENSOR REMARK 3 L11: 4.8373 L22: 4.0726 REMARK 3 L33: 1.6902 L12: 4.1359 REMARK 3 L13: 2.3277 L23: 2.5432 REMARK 3 S TENSOR REMARK 3 S11: 0.1406 S12: -0.0426 S13: -1.0020 REMARK 3 S21: 0.2572 S22: 0.1037 S23: -1.1835 REMARK 3 S31: 0.1798 S32: 0.7689 S33: -0.2443 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): 6.8707 -5.5992 30.8263 REMARK 3 T TENSOR REMARK 3 T11: -0.1615 T22: -0.1055 REMARK 3 T33: -0.0998 T12: -0.0513 REMARK 3 T13: 0.0298 T23: -0.0311 REMARK 3 L TENSOR REMARK 3 L11: 2.7646 L22: 3.8246 REMARK 3 L33: 1.6009 L12: -0.6004 REMARK 3 L13: -0.4439 L23: -0.1270 REMARK 3 S TENSOR REMARK 3 S11: -0.0903 S12: 0.2936 S13: -0.2885 REMARK 3 S21: -0.2388 S22: 0.0367 S23: -0.0937 REMARK 3 S31: 0.1495 S32: 0.1754 S33: 0.0536 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): -10.0044 -10.3863 26.2897 REMARK 3 T TENSOR REMARK 3 T11: -0.0661 T22: -0.0976 REMARK 3 T33: -0.1179 T12: -0.0809 REMARK 3 T13: -0.0328 T23: -0.0208 REMARK 3 L TENSOR REMARK 3 L11: 1.1394 L22: 1.3837 REMARK 3 L33: 2.9150 L12: 0.0316 REMARK 3 L13: -0.3778 L23: -0.0549 REMARK 3 S TENSOR REMARK 3 S11: -0.0666 S12: 0.2779 S13: -0.1267 REMARK 3 S21: -0.3497 S22: 0.0427 S23: 0.1099 REMARK 3 S31: 0.3007 S32: -0.2983 S33: 0.0239 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): -22.1743 2.7067 32.2621 REMARK 3 T TENSOR REMARK 3 T11: 0.1536 T22: 0.4810 REMARK 3 T33: 0.4294 T12: -0.0631 REMARK 3 T13: -0.1857 T23: 0.0816 REMARK 3 L TENSOR REMARK 3 L11: 0.0517 L22: 15.4780 REMARK 3 L33: 0.7177 L12: 0.8945 REMARK 3 L13: -0.1926 L23: -3.3330 REMARK 3 S TENSOR REMARK 3 S11: 0.2106 S12: 1.0280 S13: -0.3097 REMARK 3 S21: -0.8325 S22: 0.2321 S23: 1.1343 REMARK 3 S31: 0.8009 S32: -0.6648 S33: -0.4428 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): -3.9075 9.9679 31.5357 REMARK 3 T TENSOR REMARK 3 T11: -0.1228 T22: -0.1626 REMARK 3 T33: -0.1107 T12: -0.0369 REMARK 3 T13: 0.0145 T23: 0.0504 REMARK 3 L TENSOR REMARK 3 L11: 2.3194 L22: 2.4705 REMARK 3 L33: 3.2445 L12: -1.6229 REMARK 3 L13: -0.3225 L23: 0.5313 REMARK 3 S TENSOR REMARK 3 S11: -0.0008 S12: 0.1467 S13: 0.2697 REMARK 3 S21: -0.1948 S22: 0.1048 S23: -0.1289 REMARK 3 S31: -0.3820 S32: -0.1795 S33: -0.1040 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 3ZV6 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_1290049142. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-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) : 0.97841 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 : 30090 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 70.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.510 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 (%): 45.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 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 90.28650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.10850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.10850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 135.42975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.10850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.10850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.14325 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.10850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.10850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 135.42975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.10850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.10850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.14325 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 90.28650 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: 22900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -176.8 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 90.28650 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 ASN A 276 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 ASN B 276 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 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. = 15.7 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 141 -121.36 -95.87 REMARK 500 SER A 142 157.94 165.86 REMARK 500 PHE A 146 -34.41 -130.57 REMARK 500 THR A 189 -162.20 -113.99 REMARK 500 PRO A 208 48.95 -71.40 REMARK 500 ASN B 86 -30.05 -134.89 REMARK 500 TYR B 92 29.65 48.59 REMARK 500 ILE B 141 -122.78 -100.59 REMARK 500 SER B 142 159.94 167.90 REMARK 500 PHE B 146 -40.16 -136.87 REMARK 500 ASN B 188 73.21 -169.05 REMARK 500 ASP B 190 87.66 -63.70 REMARK 500 ASN B 274 72.90 53.42 REMARK 500 REMARK 500 REMARK: NULL 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 1276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 1276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4HB A 1277 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: 3ZV5 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 2,3- 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 3ZV6 A 1 281 UNP Q46381 BPHB_COMTE 1 281 DBREF 3ZV6 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 A1276 44 HET 4HB A1277 14 HET NAD B1276 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 4HB 4,4'-DIHYDROXYBIPHENYL FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 4HB C12 H10 O2 FORMUL 6 HOH *182(H2 O) HELIX 1 1 SER A 15 GLU A 28 1 14 HELIX 2 2 SER A 38 HIS A 49 1 12 HELIX 3 3 SER A 62 GLY A 78 1 17 HELIX 4 4 ALA A 95 LEU A 99 5 5 HELIX 5 5 LYS A 103 VAL A 116 1 14 HELIX 6 6 VAL A 116 ARG A 134 1 19 HELIX 7 7 SER A 142 PHE A 146 5 5 HELIX 8 8 GLY A 152 ALA A 174 1 23 HELIX 9 9 PRO A 194 GLY A 198 5 5 HELIX 10 10 SER A 203 VAL A 207 5 5 HELIX 11 11 PRO A 208 LEU A 213 1 6 HELIX 12 12 LYS A 214 VAL A 216 5 3 HELIX 13 13 ALA A 224 TYR A 228 5 5 HELIX 14 14 THR A 229 THR A 237 1 9 HELIX 15 15 THR A 237 LEU A 242 1 6 HELIX 16 16 GLY A 254 ARG A 258 5 5 HELIX 17 17 ASP A 268 LEU A 273 1 6 HELIX 18 18 SER B 15 GLU B 28 1 14 HELIX 19 19 SER B 38 GLY B 50 1 13 HELIX 20 20 SER B 62 GLY B 78 1 17 HELIX 21 21 ALA B 95 LEU B 99 5 5 HELIX 22 22 LYS B 103 VAL B 116 1 14 HELIX 23 23 VAL B 116 SER B 133 1 18 HELIX 24 24 SER B 142 PHE B 146 5 5 HELIX 25 25 GLY B 152 ALA B 174 1 23 HELIX 26 26 LEU B 209 ASP B 211 5 3 HELIX 27 27 MET B 212 LEU B 217 1 6 HELIX 28 28 ALA B 224 GLU B 227 5 4 HELIX 29 29 TYR B 228 THR B 237 1 10 HELIX 30 30 GLY B 254 ARG B 258 5 5 HELIX 31 31 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 2.11 CISPEP 2 ALA B 174 PRO B 175 0 1.22 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 ASN A 86 GLY A 88 TYR A 119 SITE 4 AC1 28 THR A 140 ILE A 141 SER A 142 TYR A 155 SITE 5 AC1 28 LYS A 159 PRO A 184 MET A 187 THR A 189 SITE 6 AC1 28 ASP A 190 LEU A 191 ILE A 204 LEU A 209 SITE 7 AC1 28 4HB A1277 HOH A2010 HOH A2021 HOH A2023 SITE 1 AC2 26 GLY B 12 SER B 15 GLY B 16 LEU B 17 SITE 2 AC2 26 GLY B 18 ASP B 36 LYS B 37 GLY B 58 SITE 3 AC2 26 ASP B 59 VAL B 60 ASN B 86 ALA B 87 SITE 4 AC2 26 GLY B 88 TYR B 119 THR B 140 ILE B 141 SITE 5 AC2 26 SER B 142 TYR B 155 LYS B 159 PRO B 184 SITE 6 AC2 26 MET B 187 THR B 189 ASP B 190 LEU B 191 SITE 7 AC2 26 ARG B 192 HOH B2066 SITE 1 AC3 9 TRP A 90 SER A 142 ASN A 143 GLY A 150 SITE 2 AC3 9 TYR A 155 LEU A 209 LEU A 213 PHE A 260 SITE 3 AC3 9 NAD A1276 CRYST1 76.217 76.217 180.573 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 0.013120 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005538 0.00000