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- PDB-2y93: Crystal Structure of cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 2y93
TitleCrystal Structure of cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB)from Pandoraea pnomenusa strain B-356.
ComponentsCIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE / SDR
Function / homology
Function and homology information


cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase activity / :
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 speciesCOMAMONAS TESTOSTERONI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 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
DepositionFeb 11, 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

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


Theoretical massNumber of molelcules
Total (without water)58,7632
Polymers58,7632
Non-polymers00
Water3,837213
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 area18400 Å2
ΔGint-147.1 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.692, 75.692, 176.876
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.65 % / Description: NONE
Crystal growDetails: 3-5 M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→69.5 Å / Num. obs: 26076 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 39.83 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.6
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.4 / % possible all: 40.6

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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: 2.22→69.5 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.471 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21889 1320 5.1 %RANDOM
Rwork0.18054 ---
obs0.18248 24478 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.985 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.22→69.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 0 213 4139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9785420
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0123.117154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72515620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1131530
X-RAY DIFFRACTIONr_chiral_restr0.0830.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.22013
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22730
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.2138
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3491.52705
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.62324178
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.95331442
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.544.51242
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: 2.225→2.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 80 -
Rwork0.256 1523 -
obs--86.42 %
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)
10.34330.158-0.10860.4738-0.34810.87160.02740.00370.06-0.0387-0.0359-0.0833-0.06130.09610.0085-0.0468-0.0170.0279-0.04860.0307-0.000116.5513.816934.165
215.31189.378513.342814.789523.207136.6172-1.10931.3439-0.275-0.95110.7115-0.2411-0.14653.23170.39780.05750.07290.12290.08540.20140.134727.96464.353139.2828
35.2304-2.442-2.495916.3239-9.02938.0358-0.4823-0.1160.28430.2115-0.1627-1.7256-0.18061.23060.645-0.1278-0.00030.09880.0154-0.01210.169620.1975-12.188534.3747
41.0727-0.29920.13272.3382-0.69250.78480.00620.1537-0.0695-0.1636-0.0418-0.17340.0556-0.00350.0356-0.0655-0.00510.0325-0.0505-0.0074-0.02988.813-5.666529.482
50.68550.1028-0.34510.6271-0.13421.0938-0.02290.1125-0.0618-0.11690.04360.01380.1023-0.1392-0.0207-0.0125-0.0279-0.0006-0.0456-0.0136-0.0574-8.8118-10.652424.8932
610.66997.98251.864515.6875-6.08976.0916-1.04231.46921.2708-1.121.79210.94090.2658-1.3363-0.7498-0.0479-0.088-0.03120.0974-0.02710.0422-21.7298-3.182528.6135
78.6697-4.8044-1.67152.96952.907213.0995-0.1714-0.3774-0.14530.01750.28370.39350.3962-0.5472-0.1124-0.05970.0375-0.0082-0.03950.0851-0.0259-14.483912.788132.8041
81.33190.2505-0.63221.0604-0.1040.92060.04850.07540.0323-0.06850.0317-0.013-0.0799-0.0659-0.0802-0.04260.02290.0123-0.03250.0494-0.0768-1.09368.581130.4622
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 DIFFRACTION7B206 - 223
8X-RAY DIFFRACTION8B224 - 275

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