10 20 30 40 50 60 70 80 2Y99 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 12-FEB-11 2Y99
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
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, COMPND 5 2\,3-DIHYDROXY-4-PHENYLHEXA-4\,6-DIENE DEHYDROGENASE, B2\,3D, COMPND 6 BIPHENYL-2\,3-DIHYDRO-2\,3-DIOL DEHYDROGENASE, BIPHENYL-CIS-DIOL COMPND 7 DEHYDROGENASE; COMPND 8 EC: 1.3.1.56; COMPND 9 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, SDR
EXPDTA X-RAY DIFFRACTION
AUTHOR S.DHINDWAL,D.N.PATIL,P.KUMAR
REVDAT 2 26-OCT-11 2Y99 1 JRNL REVDAT 1 31-AUG-11 2Y99 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 CIS-BIPHENYL-2,3-DIHYDRODIOL REMARK 1 TITL 3 -2,3-DEHYDROGENASE FROM PANDORAEA PNOMENUSA B-356. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 66 1517 2010 REMARK 1 REFN ISSN 1744-3091 REMARK 1 PMID 21045310 REMARK 1 DOI 10.1107/S1744309110036894
REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 98.17 REMARK 3 NUMBER OF REFLECTIONS : 17483 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) : 0.22003 REMARK 3 R VALUE (WORKING SET) : 0.21660 REMARK 3 FREE R VALUE : 0.28631 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 911 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) : 2.500 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.561 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1215 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.301 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.384 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3913 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.516 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.790 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40 REMARK 3 B22 (A**2) : -0.40 REMARK 3 B33 (A**2) : 0.80 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.651 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.361 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.287 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.354 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.904 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.822 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4079 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5548 ; 0.972 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 530 ; 4.610 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;37.131 ;23.117 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 618 ;15.094 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;14.007 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 640 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2183 ; 0.163 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2772 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.095 ; 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): 121 ; 0.143 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.089 ; 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): 2704 ; 0.212 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4160 ; 0.380 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1561 ; 0.341 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1388 ; 0.636 ; 4.500 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 : 8 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 186 REMARK 3 ORIGIN FOR THE GROUP (A): 15.6908 14.2165 34.3756 REMARK 3 T TENSOR REMARK 3 T11: 0.0235 T22: 0.0046 REMARK 3 T33: 0.0398 T12: -0.0186 REMARK 3 T13: 0.0045 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 0.0885 L22: 0.1489 REMARK 3 L33: 0.4197 L12: 0.1079 REMARK 3 L13: -0.1422 L23: -0.1159 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: 0.0060 S13: 0.0371 REMARK 3 S21: -0.0526 S22: 0.0192 S23: -0.0469 REMARK 3 S31: -0.0157 S32: 0.0329 S33: -0.0218 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 187 A 198 REMARK 3 ORIGIN FOR THE GROUP (A): 27.7549 5.1915 39.9378 REMARK 3 T TENSOR REMARK 3 T11: -0.0112 T22: -0.0084 REMARK 3 T33: 0.1526 T12: -0.1265 REMARK 3 T13: 0.0352 T23: 0.0199 REMARK 3 L TENSOR REMARK 3 L11: 7.6364 L22: 0.6310 REMARK 3 L33: 0.0263 L12: -2.1951 REMARK 3 L13: -0.4485 L23: 0.1289 REMARK 3 S TENSOR REMARK 3 S11: -0.4488 S12: 0.2999 S13: -0.6768 REMARK 3 S21: 0.3556 S22: 0.3693 S23: -0.2425 REMARK 3 S31: 0.3205 S32: -0.2918 S33: 0.0795 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 207 A 223 REMARK 3 ORIGIN FOR THE GROUP (A): 19.4268 -11.9125 34.9344 REMARK 3 T TENSOR REMARK 3 T11: 0.0363 T22: -0.0333 REMARK 3 T33: 0.1277 T12: -0.0365 REMARK 3 T13: 0.0097 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 4.5427 L22: 4.6831 REMARK 3 L33: 0.9303 L12: -3.2865 REMARK 3 L13: -0.9829 L23: -0.5751 REMARK 3 S TENSOR REMARK 3 S11: -0.1595 S12: -0.2101 S13: 0.1382 REMARK 3 S21: -0.0593 S22: 0.2591 S23: -0.4410 REMARK 3 S31: -0.0458 S32: 0.0977 S33: -0.0996 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 : A 224 A 275 REMARK 3 ORIGIN FOR THE GROUP (A): 7.9630 -5.3567 30.2027 REMARK 3 T TENSOR REMARK 3 T11: 0.0057 T22: -0.0069 REMARK 3 T33: 0.0408 T12: -0.0270 REMARK 3 T13: -0.0148 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.5489 L22: 0.1282 REMARK 3 L33: 0.4470 L12: 0.1760 REMARK 3 L13: -0.3044 L23: 0.0302 REMARK 3 S TENSOR REMARK 3 S11: -0.0503 S12: 0.0363 S13: -0.0875 REMARK 3 S21: -0.0963 S22: 0.1097 S23: -0.0399 REMARK 3 S31: -0.0506 S32: 0.0597 S33: -0.0594 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 1 B 186 REMARK 3 ORIGIN FOR THE GROUP (A): -9.6934 -10.3779 26.0956 REMARK 3 T TENSOR REMARK 3 T11: 0.0174 T22: 0.0047 REMARK 3 T33: 0.0241 T12: -0.0162 REMARK 3 T13: -0.0048 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.3070 L22: 0.0997 REMARK 3 L33: 0.6885 L12: -0.0500 REMARK 3 L13: -0.0773 L23: -0.0093 REMARK 3 S TENSOR REMARK 3 S11: -0.0045 S12: 0.0262 S13: -0.0078 REMARK 3 S21: -0.0312 S22: 0.0295 S23: 0.0004 REMARK 3 S31: 0.0389 S32: -0.0325 S33: -0.0250 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 187 B 198 REMARK 3 ORIGIN FOR THE GROUP (A): -23.0091 -3.1096 30.1203 REMARK 3 T TENSOR REMARK 3 T11: -0.0058 T22: 0.1153 REMARK 3 T33: 0.0628 T12: -0.1767 REMARK 3 T13: -0.0155 T23: -0.0808 REMARK 3 L TENSOR REMARK 3 L11: 1.3583 L22: 4.1984 REMARK 3 L33: 6.8064 L12: -1.1548 REMARK 3 L13: -0.7737 L23: -3.8673 REMARK 3 S TENSOR REMARK 3 S11: -0.2134 S12: -0.2411 S13: 0.2488 REMARK 3 S21: -0.6400 S22: 0.2300 S23: 0.6363 REMARK 3 S31: 0.1798 S32: 0.4618 S33: -0.0165 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 207 B 223 REMARK 3 ORIGIN FOR THE GROUP (A): -15.0176 13.4555 33.3609 REMARK 3 T TENSOR REMARK 3 T11: -0.0027 T22: -0.0115 REMARK 3 T33: 0.0601 T12: 0.0150 REMARK 3 T13: 0.0018 T23: 0.0472 REMARK 3 L TENSOR REMARK 3 L11: 5.3856 L22: 0.9799 REMARK 3 L33: 3.5595 L12: -0.4433 REMARK 3 L13: -2.5215 L23: 1.7057 REMARK 3 S TENSOR REMARK 3 S11: -0.1899 S12: -0.1845 S13: -0.4504 REMARK 3 S21: -0.0175 S22: -0.0099 S23: 0.1520 REMARK 3 S31: -0.2670 S32: -0.1294 S33: 0.1998 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 224 B 275 REMARK 3 ORIGIN FOR THE GROUP (A): -1.9870 8.9321 31.1586 REMARK 3 T TENSOR REMARK 3 T11: 0.0411 T22: -0.0088 REMARK 3 T33: 0.0251 T12: -0.0067 REMARK 3 T13: -0.0010 T23: 0.0170 REMARK 3 L TENSOR REMARK 3 L11: 0.8674 L22: 0.3351 REMARK 3 L33: 0.2765 L12: -0.1422 REMARK 3 L13: -0.2110 L23: 0.2995 REMARK 3 S TENSOR REMARK 3 S11: 0.0153 S12: 0.0922 S13: 0.0315 REMARK 3 S21: -0.0044 S22: 0.0023 S23: 0.0134 REMARK 3 S31: -0.0303 S32: -0.0432 S33: -0.0177 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 REMARK 3 RIDING POSITIONS.
REMARK 4 REMARK 4 2Y99 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-FEB-11. REMARK 100 THE PDBE ID CODE IS EBI-47355.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER MICROSTAR-H REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE (MAR345) REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18429 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.50 REMARK 200 RESOLUTION RANGE LOW (A) : 10.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.7 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.70 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 10.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.5 REMARK 200 R MERGE FOR SHELL (I) : 0.25 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.40 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 (%): 40.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 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 89.99500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.07000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 134.99250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.07000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.07000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.99750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.07000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.07000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 134.99250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.07000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.07000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.99750 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 89.99500 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: 23250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -171.2 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 89.99500
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 LEU A 199 REMARK 465 SER A 200 REMARK 465 GLU A 201 REMARK 465 GLN A 202 REMARK 465 SER A 203 REMARK 465 ILE A 204 REMARK 465 SER A 205 REMARK 465 SER A 206 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 SER B 206 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 B 276 CA C O CB CG OD1 ND2
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 -124.26 -105.35 REMARK 500 SER A 142 156.01 173.45 REMARK 500 PHE A 146 -34.12 -142.23 REMARK 500 ASP A 190 48.71 -108.54 REMARK 500 TYR B 92 16.06 59.89 REMARK 500 ILE B 141 -125.72 -95.37 REMARK 500 SER B 142 162.89 173.27 REMARK 500 PHE B 146 -36.39 -138.20 REMARK 500 SER B 195 2.50 -67.70 REMARK 500 ASP B 268 58.54 -98.35 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 A1276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B1276
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZV5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, REMARK 900 3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B REMARK 900 -356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT 2,3- REMARK 900 DIHYDROXYBIPHENYL REMARK 900 RELATED ID: 3ZV6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, REMARK 900 3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B REMARK 900 -356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT ANALOG REMARK 900 4,4'-DIHYDROXYBIPHENYL REMARK 900 RELATED ID: 2Y93 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, REMARK 900 3-DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B REMARK 900 -356. REMARK 900 RELATED ID: 3ZV4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, REMARK 900 3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B REMARK 900 -356 IN APO FORM AT 1.8 ANGSTROM REMARK 900 RELATED ID: 3ZV3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, REMARK 900 3-DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B REMARK 900 -356 IN INTERMEDIATE STATE OF SUBSTRATE BINDING LOOP
DBREF 2Y99 A 1 281 UNP Q46381 BPHB_COMTE 1 281 DBREF 2Y99 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 NAD B1276 44
HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE
FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 HOH *250(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 208 SER A 215 1 8 HELIX 10 10 ALA A 224 TYR A 228 5 5 HELIX 11 11 THR A 229 THR A 237 1 9 HELIX 12 12 GLY A 254 ARG A 258 5 5 HELIX 13 13 ASP A 268 LEU A 273 1 6 HELIX 14 14 SER B 15 GLU B 28 1 14 HELIX 15 15 SER B 38 GLY B 50 1 13 HELIX 16 16 SER B 62 GLY B 78 1 17 HELIX 17 17 ALA B 95 LEU B 99 5 5 HELIX 18 18 LYS B 103 VAL B 116 1 14 HELIX 19 19 VAL B 116 ARG B 134 1 19 HELIX 20 20 SER B 142 PHE B 146 5 5 HELIX 21 21 GLY B 152 LEU B 173 1 22 HELIX 22 22 LEU B 209 ASP B 211 5 3 HELIX 23 23 MET B 212 LEU B 217 1 6 HELIX 24 24 ALA B 224 TYR B 228 5 5 HELIX 25 25 THR B 229 THR B 237 1 9 HELIX 26 26 THR B 237 LEU B 242 1 6 HELIX 27 27 GLY B 254 ARG B 258 5 5
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 3.68 CISPEP 2 ALA B 174 PRO B 175 0 5.47
SITE 1 AC1 22 GLY A 12 SER A 15 GLY A 16 LEU A 17 SITE 2 AC1 22 ASP A 36 LYS A 37 GLY A 58 ASP A 59 SITE 3 AC1 22 VAL A 60 ARG A 61 ASN A 86 GLY A 88 SITE 4 AC1 22 ILE A 141 SER A 142 TYR A 155 LYS A 159 SITE 5 AC1 22 PRO A 184 MET A 187 THR A 189 ASP A 190 SITE 6 AC1 22 LEU A 191 HOH A2115 SITE 1 AC2 23 GLY B 12 SER B 15 GLY B 16 LEU B 17 SITE 2 AC2 23 ASP B 36 LYS B 37 GLY B 58 ASP B 59 SITE 3 AC2 23 VAL B 60 ASN B 86 GLY B 88 ILE B 141 SITE 4 AC2 23 SER B 142 TYR B 155 LYS B 159 PRO B 184 SITE 5 AC2 23 MET B 187 THR B 189 ASP B 190 LEU B 191 SITE 6 AC2 23 ARG B 192 HOH B2006 HOH B2098
CRYST1 76.140 76.140 179.990 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 0.013134 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013134 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005556 0.00000