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- PDB-3zv4: CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENA... -

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Basic information

Entry
Database: PDB / ID: 3zv4
TitleCRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 IN APO FORM AT 1.8 ANGSTROM
ComponentsCIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE/OXIDOREDUCTASE / SDR / COMAMONAS TESTOSTERONI
Function / homology
Function and homology information


cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase activity / catabolic process
Similarity search - Function
Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / : / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
Similarity search - Component
Biological speciesPANDORAEA PNOMENUSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDhindwal, S. / Patil, D.N. / Kumar, P.
Citation
Journal: J.Biol.Chem. / Year: 2011
Title: Biochemical Studies and Ligand-Bound Structures of Biphenyl Dehydrogenase from Pandoraea Pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme.
Authors: Dhindwal, S. / Patil, D.N. / Mohammadi, M. / Sylvestre, M. / Tomar, S. / Kumar, P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Expression, Purification, Crystallization and Preliminary Crystallographic Studies of Cis-Biphenyl-2,3-Dihydrodiol-2,3-Dehydrogenase from Pandoraea Pnomenusa B-356.
Authors: Patil, D.N. / Tomar, S. / Sylvestre, M. / Kumar, P.
History
DepositionJul 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
B: CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)58,7632
Polymers58,7632
Non-polymers00
Water9,404522
1
A: CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
B: CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE

A: CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
B: CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)117,5264
Polymers117,5264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area18340 Å2
ΔGint-149.8 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.784, 75.784, 181.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-2066-

HOH

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Components

#1: Protein CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE / 2 / 3-DIHYDRO-2 / 3-DIHYDROXYBIPHENYL DEHYDROGENASE / 2 / 3-DIHYDROXY-4-PHENYLHEXA-4 / 6-DIENE ...2 / 3-DIHYDRO-2 / 3-DIHYDROXYBIPHENYL DEHYDROGENASE / 2 / 3-DIHYDROXY-4-PHENYLHEXA-4 / 6-DIENE DEHYDROGENASE / B2\ / 3D / BIPHENYL-2 / 3-DIHYDRO-2 / 3-DIOL DEHYDROGENASE / BIPHENYL-CIS-DIOL DEHYDROGENASE


Mass: 29381.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PANDORAEA PNOMENUSA (bacteria) / Strain: B-356 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q46381, cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.37 % / Description: NONE
Crystal growDetails: SODIUM MALONATE, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2011
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97841 Å / Relative weight: 1
ReflectionResolution: 1.58→100 Å / Num. obs: 73356 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 26.701 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 1.8→70.01 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.44 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BDB

1bdb


Resolution: 1.8→70.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.174 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22736 2489 5 %RANDOM
Rwork0.19113 ---
obs0.19297 47247 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.433 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→70.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 0 522 4424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223980
X-RAY DIFFRACTIONr_bond_other_d0.0010.022660
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9765397
X-RAY DIFFRACTIONr_angle_other_deg0.93836476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9115530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15723.072153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35315618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2321530
X-RAY DIFFRACTIONr_chiral_restr0.070.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
X-RAY DIFFRACTIONr_nbd_refined0.20.2935
X-RAY DIFFRACTIONr_nbd_other0.1930.23013
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22033
X-RAY DIFFRACTIONr_nbtor_other0.0850.22021
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2367
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6091.53339
X-RAY DIFFRACTIONr_mcbond_other0.1261.51108
X-RAY DIFFRACTIONr_mcangle_it0.72124159
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.431541
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.964.51238
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 204 -
Rwork0.25 3428 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.00320.1221-0.5711.137-0.63121.47660.02880.10740.1078-0.0796-0.0222-0.1603-0.06080.1573-0.0066-0.1351-0.03960.0126-0.13590.034-0.115715.713214.223334.6079
222.10468.066711.59847.35254.617620.1805-0.21051.73230.1432-0.45821.1552-0.396-1.01051.953-0.94470.17480.1130.07590.23910.09240.33427.5545.860540.7777
314.8257-3.15063.38254.6429-2.70185.7418-0.4803-0.21380.38930.2051-0.121-0.83160.1231.14430.60120.040.03780.06930.0201-0.02990.148519.1877-12.101535.2695
41.7236-0.60780.00322.6775-0.17511.1009-0.06760.2519-0.2106-0.20290.0414-0.05210.16390.09990.0261-0.1405-0.01730.0188-0.0748-0.0148-0.0937.7653-5.416330.7164
50.9959-0.0823-0.33470.93490.0152.1395-0.06030.2806-0.119-0.23010.04540.10990.1494-0.25970.0148-0.1031-0.0588-0.015-0.0951-0.0244-0.1306-9.855-10.461526.6092
66.256810.8372-4.76223.8725-12.98218.0169-0.32731.45370.0794-1.11231.06391.19450.2627-1.5148-0.73660.1578-0.0443-0.00260.2598-0.01790.2349-22.7465-3.193130.7402
72.9019-2.16740.46851.68970.36477.2743-0.077-0.186-0.1380.04720.14910.4440.1186-0.5564-0.0722-0.10250.01840.018-0.05610.1012-0.0746-14.752613.689233.6195
82.1114-1.0017-0.43841.78130.55331.762-0.01160.07050.2215-0.1720.1435-0.0919-0.28570.0139-0.1319-0.1297-0.02820.0223-0.12160.0305-0.1428-1.95518.83231.6676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 186
2X-RAY DIFFRACTION2A187 - 197
3X-RAY DIFFRACTION3A207 - 223
4X-RAY DIFFRACTION4A224 - 275
5X-RAY DIFFRACTION5B1 - 186
6X-RAY DIFFRACTION6B187 - 197
7X-RAY DIFFRACTION7B207 - 223
8X-RAY DIFFRACTION8B224 - 275

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