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- PDB-3zv5: CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENA... -

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Basic information

Entry
Database: PDB / ID: 3zv5
TitleCRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT 2,3-DIHYDROXYBIPHENYL
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
BIPHENYL-2,3-DIOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
Similarity search - Component
Biological speciesPANDORAEA PNOMENUSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2765
Polymers58,7632
Non-polymers1,5133
Water2,378132
1
A: CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
B: CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)120,55210
Polymers117,5264
Non-polymers3,0266
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area24100 Å2
ΔGint-183.3 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.394, 75.394, 173.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-BPY / BIPHENYL-2,3-DIOL


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.13 Å3/Da / Density % sol: 42.19 % / 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: 0.97625
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2011
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 20162 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 12.1 % / Biso Wilson estimate: 47.592 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.32
Reflection shellResolution: 2.4→69.17 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.29 / % possible all: 99.4

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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: 2.4→69.17 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.43 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.935 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26568 982 5.1 %RANDOM
Rwork0.20762 ---
obs0.21059 18141 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.265 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2--1.68 Å20 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.4→69.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 102 132 4212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7762.015659
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9523.205156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53815631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1361530
X-RAY DIFFRACTIONr_chiral_restr0.1170.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023134
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.22177
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22795
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.2120
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6191.52747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01424238
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.80331639
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7444.51421
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: 2.403→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 78 -
Rwork0.277 1306 -
obs--94.09 %
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)
11.21570.04-0.56780.95770.33561.35780.0150.114-0.0956-0.11980.0015-0.05150.24470.2854-0.0165-0.05720.0678-0.0073-0.0228-0.0108-0.122813.6784-16.9687-9.6446
22.5728-1.86182.43441.9467-0.89173.56610.28740.0002-0.7881-0.10280.06650.46570.4273-0.0873-0.35390.08190.03730.02850.01710.01770.1234-2.4172-25.8341-8.2018
32.68240.6842-0.1841.9792-0.01711.8151-0.04360.24890.0615-0.25040.05080.21860.1917-0.1532-0.0071-0.03460.0316-0.0268-0.10740.0075-0.1068-6.2291-8.4448-14.2014
41.30640.38650.44690.93630.24642.1947-0.03350.13390.0522-0.21720.01330.0384-0.2657-0.13360.0202-0.05340.04390.0019-0.09440.0305-0.1261-10.68448.3899-19.516
52.0096-0.58210.82340.1686-0.23850.33740.1474-0.16411.90830.57550.0833-0.4788-0.74530.0164-0.23060.60050.1090.09920.2287-0.01750.45722.499320.7114-13.3023
62.48650.2373-0.22152.1318-0.09351.71890.01060.0590.1968-0.0534-0.0132-0.1578-0.20480.32110.0026-0.0638-0.00780.0313-0.07950.0107-0.13079.42912.2016-13.4106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 185
2X-RAY DIFFRACTION2A186 - 226
3X-RAY DIFFRACTION3A227 - 275
4X-RAY DIFFRACTION4B1 - 185
5X-RAY DIFFRACTION5B186 - 213
6X-RAY DIFFRACTION6B214 - 275

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