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- PDB-1eil: 2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE -

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Basic information

Entry
Database: PDB / ID: 1eil
Title2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE
Components2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE / four repetitions of beta-alpha-beta-beta-beta motifs
Function / homology
Function and homology information


biphenyl-2,3-diol 1,2-dioxygenase / biphenyl-2,3-diol 1,2-dioxygenase activity / xenobiotic catabolic process / ferrous iron binding
Similarity search - Function
2,3-dihydroxybiphenyl 1,2-dioxygenase / Dihydroxybiphenyl dioxygenase BphC D1 / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. ...2,3-dihydroxybiphenyl 1,2-dioxygenase / Dihydroxybiphenyl dioxygenase BphC D1 / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / Biphenyl-2,3-diol 1,2-dioxygenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSenda, T.
Citation
Journal: J.Inorg.Biochem. / Year: 2001
Title: Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase.
Authors: Uragami, Y. / Senda, T. / Sugimoto, K. / Sato, N. / Nagarajan, V. / Masai, E. / Fukuda, M. / Mitsu, Y.
#1: Journal: PROC.JPN.ACAD.,SER.B / Year: 1995
Title: Three-dimensional Structure of 2,3-dihydroxybiphenyl dioxygenase (BphC enzyme) from Pseudomonas sp. strain KKS102 having Polychlorinated Biphenyl (PCB) Degrading Activity.
Authors: Sugiyama, K. / Senda, T. / Kimbara, K. / Fukuda, M. / Mitsui, Y.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102.
Authors: Senda, T. / Sugiyama, K. / Narita, H. / Yamamoto, T. / Kimbara, K. / Fukuda, M. / Sato, M. / Yano, K. / Mitsui, Y.
History
DepositionFeb 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3033
Polymers32,1521
Non-polymers1522
Water3,477193
1
A: 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)258,42824
Polymers257,2128
Non-polymers1,21516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area20220 Å2
ΔGint-357 kcal/mol
Surface area76710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.750, 121.750, 108.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE / BIPHENYL-2 / 3-DIOL 1 / 2-DIOXYGENASE / 23 OHBP OXYGENASE / DHBD


Mass: 32151.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: KKS102 / Plasmid: PHNA2 / Production host: Escherichia coli (E. coli)
References: UniProt: P17297, biphenyl-2,3-diol 1,2-dioxygenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSubstrate free form. Structure determined under anaerobic condition (active form structure)

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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: 3.14 Å3/Da / Density % sol: 60.77 %
Crystal growTemperature: 285 K / pH: 7.5
Details: 285 K, Tris/HCl Ammonium sulfate hexylene glycol, pH 7.5, temperature 285.0K
Crystal grow
*PLUS
Temperature: 12 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
2100 mMTris-HCl11
327.7 %satammonium sulfate11
418 %(v/v)hexylene glycol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 115926 / Num. obs: 32373 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.255 / % possible all: 100
Reflection
*PLUS
Num. obs: 27837 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→40 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.253 1349 Random
Rwork0.206 --
all0.209 26935 -
obs0.209 26935 -
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 6 193 2439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.35
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection all: 27837 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg2.4

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