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- PDB-3zv3: CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENA... -

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Basic information

Entry
Database: PDB / ID: 3zv3
TitleCRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B-356 IN INTERMEDIATE STATE OF SUBSTRATE BINDING LOOP
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / pdbx_struct_special_symmetry
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
Water70339
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_554-y,-x,-z-1/21
Buried area18450 Å2
ΔGint-142.1 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.735, 75.735, 178.947
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
11A-2019-

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.: 39 / 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: 2.21 Å3/Da / Density % sol: 44.43 % / Description: NONE
Crystal growDetails: SODIUM MALONATE, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2010 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 13445 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 70.134 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.44
Reflection shellResolution: 2.9→69.67 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.08 / % possible all: 98.3

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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: 2.9→69.67 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.864 / SU B: 23.302 / SU ML: 0.427 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2946 601 5 %RANDOM
Rwork0.26788 ---
obs0.26917 11486 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.376 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2---2.11 Å20 Å2
3---4.21 Å2
Refinement stepCycle: LAST / Resolution: 2.9→69.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 0 39 3955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223986
X-RAY DIFFRACTIONr_bond_other_d0.0060.022654
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9765408
X-RAY DIFFRACTIONr_angle_other_deg0.86736467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4515531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05823.247154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85415621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9131529
X-RAY DIFFRACTIONr_chiral_restr0.0510.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02808
X-RAY DIFFRACTIONr_nbd_refined0.1940.2883
X-RAY DIFFRACTIONr_nbd_other0.2020.22920
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21937
X-RAY DIFFRACTIONr_nbtor_other0.0840.22142
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 45 -
Rwork0.386 819 -
obs--98.52 %

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