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- PDB-1bdb: CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS S... -

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Basic information

Entry
Database: PDB / ID: 1bdb
TitleCIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS SP. LB400
ComponentsCIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD-DEPENDENT OXIDOREDUCTASE / SHORT-CHAIN ALCOHOL DEHYDROGENASE / PCB DEGRADATION
Function / homology
Function and homology information


cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase activity / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHuelsmeyer, M. / Hecht, H.-J. / Niefind, K. / Hofer, B. / Timmis, K.N. / Schomburg, D.
Citation
Journal: Protein Sci. / Year: 1998
Title: Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution.
Authors: Hulsmeyer, M. / Hecht, H.J. / Niefind, K. / Hofer, B. / Eltis, L.D. / Timmis, K.N. / Schomburg, D.
#1: Journal: Gene / Year: 1993
Title: Genetic Analysis of a Pseudomonas Locus Encoding a Pathway for Biphenyl/Polychlorinated Biphenyl Degradation
Authors: Hofer, B. / Eltis, L.D. / Dowling, D.N. / Timmis, K.N.
History
DepositionMay 10, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5932
Polymers28,9301
Non-polymers6631
Water2,162120
1
A: CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE
hetero molecules

A: CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE
hetero molecules

A: CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE
hetero molecules

A: CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3738
Polymers115,7194
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area23210 Å2
ΔGint-179 kcal/mol
Surface area32140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.200, 79.200, 152.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE


Mass: 28929.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas sp. (bacteria) / Cellular location: CYTOPLASM / Variant: PLEBD4 / Strain: LB400 / References: UniProt: P47227
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M CITRATE/PHOSPHATE BUFFER, PH 7.5, 1.2 M AMMONIUM SULFATE CONTAINING 50 MM NAD
Crystal grow
*PLUS
Temperature: 12 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMcitrate1reservoir
21.2 Mammonium sulfate1reservoir
333 mMcitrate1drop
40.4 Mammonium sulfate1drop
54 mg/mlprotain1drop
617 mMNAD+1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 2, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 18861 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.067 / Net I/σ(I): 22.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 14.4 / Rsym value: 0.188 / % possible all: 94
Reflection
*PLUS
Num. measured all: 19980 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Lowest resolution: 2.08 Å / % possible obs: 94 % / Rmerge(I) obs: 0.188

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HSD

2hsd


Resolution: 2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 966 5 %RANDOM
Rwork0.179 ---
obs-17895 94.4 %-
Displacement parametersBiso mean: 17.6 Å2
Refine analyzeLuzzati sigma a obs: 0.08 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 44 120 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.391.39
X-RAY DIFFRACTIONp_mcangle_it22
X-RAY DIFFRACTIONp_scbond_it1.731.73
X-RAY DIFFRACTIONp_scangle_it2.782.78
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.0990.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2640.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor17.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor37.320
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 18861 / Rfactor all: 0.179 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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