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- PDB-3zv6: CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENA... -

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Basic information

Entry
Database: PDB / ID: 3zv6
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 ANALOG 4,4'-DIHYDROXYBIPHENYL
ComponentsCIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE/OXIDOREDUCTASE / SDR
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
4,4'-DIHYDROXYBIPHENYL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
Similarity search - Component
Biological speciesCOMAMONAS TESTOSTERONI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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
Water3,279182
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 operation8_555-y,-x,-z+1/21
Buried area22900 Å2
ΔGint-176.8 kcal/mol
Surface area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.217, 76.217, 180.573
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.) COMAMONAS TESTOSTERONI (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-4HB / 4,4'-DIHYDROXYBIPHENYL


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.: 182 / 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: 2.26 Å3/Da / Density % sol: 45.63 % / 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: 2.15→100 Å / Num. obs: 30090 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 38.421 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.34
Reflection shellResolution: 2.15→70.19 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.51 / % 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: 2.14→70.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.885 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22654 1509 5.1 %RANDOM
Rwork0.18638 ---
obs0.18845 28211 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.406 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.14→70.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 102 182 4260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224169
X-RAY DIFFRACTIONr_bond_other_d0.0020.022758
X-RAY DIFFRACTIONr_angle_refined_deg1.5112.0095672
X-RAY DIFFRACTIONr_angle_other_deg1.0523.0036659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0123.185157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23815632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3611530
X-RAY DIFFRACTIONr_chiral_restr0.0890.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02837
X-RAY DIFFRACTIONr_nbd_refined0.2020.2935
X-RAY DIFFRACTIONr_nbd_other0.1990.23135
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22044
X-RAY DIFFRACTIONr_nbtor_other0.090.22149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2156
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7131.53399
X-RAY DIFFRACTIONr_mcbond_other0.1531.51127
X-RAY DIFFRACTIONr_mcangle_it0.90424240
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63931753
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.354.51431
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: 2.143→2.198 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 110 -
Rwork0.245 1971 -
obs--95.33 %
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)
11.11630.2213-0.49211.1865-0.38051.9252-0.00650.12910.133-0.13870.0057-0.153-0.20390.2840.0008-0.1032-0.09620.0299-0.10310.0265-0.095615.41514.5134.3361
24.83734.13592.32774.07262.54321.69020.1406-0.0426-1.0020.25720.1037-1.18350.17980.7689-0.24430.05340.01040.08250.24530.04650.296824.4337-1.51336.2585
32.7646-0.6004-0.44393.8246-0.1271.6009-0.09030.2936-0.2885-0.23880.0367-0.09370.14950.17540.0536-0.1615-0.05130.0298-0.1055-0.0311-0.09986.8707-5.599230.8263
41.13940.0316-0.37781.3837-0.05492.915-0.06660.2779-0.1267-0.34970.04270.10990.3007-0.29830.0239-0.0661-0.0809-0.0328-0.0976-0.0208-0.1179-10.0044-10.386326.2897
50.05170.8945-0.192615.478-3.3330.71770.21061.028-0.3097-0.83250.23211.13430.8009-0.6648-0.44280.1536-0.0631-0.18570.4810.08160.4294-22.17432.706732.2621
62.3194-1.6229-0.32252.47050.53133.2445-0.00080.14670.2697-0.19480.1048-0.1289-0.382-0.1795-0.104-0.1228-0.03690.0145-0.16260.0504-0.1107-3.90759.967931.5357
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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