10 20 30 40 50 60 70 80 3ZV4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 23-JUL-11 3ZV4
TITLE CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3- TITLE 2 DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B- TITLE 3 356 IN APO FORM AT 1.8 ANGSTROM
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: 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 2 26-OCT-11 3ZV4 1 JRNL REVDAT 1 31-AUG-11 3ZV4 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- REMARK 1 TITL 3 BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PANDORAEA REMARK 1 TITL 4 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.44 REMARK 3 NUMBER OF REFLECTIONS : 47247 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) : 0.19297 REMARK 3 R VALUE (WORKING SET) : 0.19113 REMARK 3 FREE R VALUE : 0.22736 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 2489 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) : 1.800 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.847 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3428 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.250 REMARK 3 BIN FREE R VALUE SET COUNT : 204 REMARK 3 BIN FREE R VALUE : 0.299 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3910 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 522 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.701 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.433 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19 REMARK 3 B22 (A**2) : -0.19 REMARK 3 B33 (A**2) : 0.39 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): 0.136 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.128 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.174 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3980 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2660 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5397 ; 1.253 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6476 ; 0.938 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 530 ; 5.911 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;36.157 ;23.072 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 618 ;14.353 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;19.232 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 620 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4526 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 810 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 935 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3013 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2033 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2021 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 367 ; 0.152 ; 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): 30 ; 0.167 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 107 ; 0.263 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.165 ; 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): 3339 ; 0.609 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1108 ; 0.126 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4159 ; 0.721 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1541 ; 1.400 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1238 ; 1.960 ; 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): 15.7132 14.2233 34.6079 REMARK 3 T TENSOR REMARK 3 T11: -0.1351 T22: -0.1359 REMARK 3 T33: -0.1157 T12: -0.0396 REMARK 3 T13: 0.0126 T23: 0.0340 REMARK 3 L TENSOR REMARK 3 L11: 1.0032 L22: 1.1370 REMARK 3 L33: 1.4766 L12: 0.1221 REMARK 3 L13: -0.5710 L23: -0.6312 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: 0.1074 S13: 0.1078 REMARK 3 S21: -0.0796 S22: -0.0222 S23: -0.1603 REMARK 3 S31: -0.0608 S32: 0.1573 S33: -0.0066 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 197 REMARK 3 ORIGIN FOR THE GROUP (A): 27.5540 5.8605 40.7777 REMARK 3 T TENSOR REMARK 3 T11: 0.1748 T22: 0.2391 REMARK 3 T33: 0.3340 T12: 0.1130 REMARK 3 T13: 0.0759 T23: 0.0924 REMARK 3 L TENSOR REMARK 3 L11: 22.1046 L22: 7.3525 REMARK 3 L33: 20.1805 L12: 8.0667 REMARK 3 L13: 11.5984 L23: 4.6176 REMARK 3 S TENSOR REMARK 3 S11: -0.2105 S12: 1.7323 S13: 0.1432 REMARK 3 S21: -0.4582 S22: 1.1552 S23: -0.3960 REMARK 3 S31: -1.0105 S32: 1.9530 S33: -0.9447 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): 19.1877 -12.1015 35.2695 REMARK 3 T TENSOR REMARK 3 T11: 0.0400 T22: 0.0201 REMARK 3 T33: 0.1485 T12: 0.0378 REMARK 3 T13: 0.0693 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 14.8257 L22: 4.6429 REMARK 3 L33: 5.7418 L12: -3.1506 REMARK 3 L13: 3.3825 L23: -2.7018 REMARK 3 S TENSOR REMARK 3 S11: -0.4803 S12: -0.2138 S13: 0.3893 REMARK 3 S21: 0.2051 S22: -0.1210 S23: -0.8316 REMARK 3 S31: 0.1230 S32: 1.1443 S33: 0.6012 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): 7.7653 -5.4163 30.7164 REMARK 3 T TENSOR REMARK 3 T11: -0.1405 T22: -0.0748 REMARK 3 T33: -0.0930 T12: -0.0173 REMARK 3 T13: 0.0188 T23: -0.0148 REMARK 3 L TENSOR REMARK 3 L11: 1.7236 L22: 2.6775 REMARK 3 L33: 1.1009 L12: -0.6078 REMARK 3 L13: 0.0032 L23: -0.1751 REMARK 3 S TENSOR REMARK 3 S11: -0.0676 S12: 0.2519 S13: -0.2106 REMARK 3 S21: -0.2029 S22: 0.0414 S23: -0.0521 REMARK 3 S31: 0.1639 S32: 0.0999 S33: 0.0261 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): -9.8550 -10.4615 26.6092 REMARK 3 T TENSOR REMARK 3 T11: -0.1031 T22: -0.0951 REMARK 3 T33: -0.1306 T12: -0.0588 REMARK 3 T13: -0.0150 T23: -0.0244 REMARK 3 L TENSOR REMARK 3 L11: 0.9959 L22: 0.9349 REMARK 3 L33: 2.1395 L12: -0.0823 REMARK 3 L13: -0.3347 L23: 0.0150 REMARK 3 S TENSOR REMARK 3 S11: -0.0603 S12: 0.2806 S13: -0.1190 REMARK 3 S21: -0.2301 S22: 0.0454 S23: 0.1099 REMARK 3 S31: 0.1494 S32: -0.2597 S33: 0.0148 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 197 REMARK 3 ORIGIN FOR THE GROUP (A): -22.7465 -3.1931 30.7402 REMARK 3 T TENSOR REMARK 3 T11: 0.1578 T22: 0.2598 REMARK 3 T33: 0.2349 T12: -0.0443 REMARK 3 T13: -0.0026 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 6.2568 L22: 23.8725 REMARK 3 L33: 8.0169 L12: 10.8372 REMARK 3 L13: -4.7620 L23: -12.9821 REMARK 3 S TENSOR REMARK 3 S11: -0.3273 S12: 1.4537 S13: 0.0794 REMARK 3 S21: -1.1123 S22: 1.0639 S23: 1.1945 REMARK 3 S31: 0.2627 S32: -1.5148 S33: -0.7366 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): -14.7526 13.6892 33.6195 REMARK 3 T TENSOR REMARK 3 T11: -0.1025 T22: -0.0561 REMARK 3 T33: -0.0746 T12: 0.0184 REMARK 3 T13: 0.0180 T23: 0.1012 REMARK 3 L TENSOR REMARK 3 L11: 2.9019 L22: 1.6897 REMARK 3 L33: 7.2743 L12: -2.1674 REMARK 3 L13: 0.4685 L23: 0.3647 REMARK 3 S TENSOR REMARK 3 S11: -0.0770 S12: -0.1860 S13: -0.1380 REMARK 3 S21: 0.0472 S22: 0.1491 S23: 0.4440 REMARK 3 S31: 0.1186 S32: -0.5564 S33: -0.0722 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): -1.9551 8.8320 31.6676 REMARK 3 T TENSOR REMARK 3 T11: -0.1297 T22: -0.1216 REMARK 3 T33: -0.1428 T12: -0.0282 REMARK 3 T13: 0.0223 T23: 0.0305 REMARK 3 L TENSOR REMARK 3 L11: 2.1114 L22: 1.7813 REMARK 3 L33: 1.7620 L12: -1.0017 REMARK 3 L13: -0.4384 L23: 0.5533 REMARK 3 S TENSOR REMARK 3 S11: -0.0116 S12: 0.0705 S13: 0.2215 REMARK 3 S21: -0.1720 S22: 0.1435 S23: -0.0919 REMARK 3 S31: -0.2857 S32: 0.0139 S33: -0.1319 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 3ZV4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-11. REMARK 100 THE PDBE ID CODE IS EBI-49149.
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 (MX-225) REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL 2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73356 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.58 REMARK 200 RESOLUTION RANGE LOW (A) : 100.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.1 REMARK 200 R MERGE (I) : 0.09 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 70.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.3 REMARK 200 R MERGE FOR SHELL (I) : 0.88 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.44 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 (%): 45.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 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 90.89100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.89200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.89200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 136.33650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.89200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.89200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.44550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.89200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.89200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 136.33650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.89200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.89200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.44550 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 90.89100 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: 18340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -149.8 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 90.89100
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B2066 LIES ON A SPECIAL POSITION.
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 190 REMARK 465 LEU A 191 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 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: 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 O THR A 237 O HOH A 2261 2.12 REMARK 500 NH1 ARG B 178 O HOH B 2136 2.00 REMARK 500 O HOH A 2048 O HOH A 2095 2.18 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 -121.08 -98.12 REMARK 500 SER A 142 157.29 168.44 REMARK 500 PHE A 146 -32.58 -132.99 REMARK 500 ALA A 183 79.92 -116.42 REMARK 500 MET A 187 -169.09 -77.19 REMARK 500 ARG A 238 107.47 -53.89 REMARK 500 TYR A 251 59.12 -142.69 REMARK 500 TYR B 92 19.69 58.34 REMARK 500 ILE B 141 -120.18 -100.79 REMARK 500 SER B 142 157.10 170.09 REMARK 500 PHE B 146 -35.04 -135.35 REMARK 500 LEU B 191 93.18 -66.54 REMARK 500 VAL B 216 -50.03 -122.59 REMARK 500 ASN B 274 -140.79 64.94 REMARK 500 REMARK 500 REMARK: NULL
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, REMARK 900 3-DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B REMARK 900 -356 COMPLEX WITH CO-ENZYME NAD 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: 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: 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 3ZV4 A 1 281 UNP Q46381 BPHB_COMTE 1 281 DBREF 3ZV4 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
FORMUL 3 HOH *522(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 VAL A 216 1 9 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 ALA B 174 1 23 HELIX 22 22 PRO B 194 GLY B 198 5 5 HELIX 23 23 LEU B 209 ASP B 211 5 3 HELIX 24 24 MET B 212 LEU B 217 1 6 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 ASN B 274 1 7
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 2.35 CISPEP 2 ALA B 174 PRO B 175 0 2.31
CRYST1 75.784 75.784 181.782 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 0.013195 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013195 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005501 0.00000