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- PDB-1kmy: Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Comple... -

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Basic information

Entry
Database: PDB / ID: 1kmy
TitleCrystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 2,3-dihydroxybiphenyl under Anaerobic Condition
Components2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE / dioxygenase / 2 / 3-dihydroxybiphenyl
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 ...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 / : / TERTIARY-BUTYL ALCOHOL / Biphenyl-2,3-diol 1,2-dioxygenase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHan, S. / Bolin, J.T.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.
Authors: Vaillancourt, F.H. / Han, S. / Fortin, P.D. / Bolin, J.T. / Eltis, L.D.
#1: Journal: TO BE PUBLISHED
Title: Definitive Evidence for Monoanionic Binding of 2,3-dihydroxybiphenyl to 2,3-dihydroxybiphenyl Dioxygenase from UV Resonance Raman Spectroscopy, UV/Vis Absorption Spectroscopy, and Crystallography.
Authors: Vaillancourt, F.H. / Barbosa, C.J. / Spiro, T.G. / Bolin, J.T. / Blades, M.W. / Turner, R.F.B. / Eltis, L.D.
#2: Journal: Science / Year: 1995
Title: Crystal Structure of the Biphenyl-cleaving Extradiol Dioxygenase from a PCB-degrading Pseudomonad.
Authors: Han, S. / Eltis, L.D. / Timmis, K.N. / Muchmore, S.W. / Bolin, J.T.
#3: Journal: Handbook of Metalloproteins / Year: 2001
Title: 2,3-Dihydroxybiphenyl 1,2-dioxygenase.
Authors: Bolin, J.T. / Eltis, L.D.
History
DepositionDec 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: 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 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,6944
Polymers32,3781
Non-polymers3163
Water2,072115
1
A: 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)261,55032
Polymers259,0218
Non-polymers2,52924
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_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area24520 Å2
ΔGint-242 kcal/mol
Surface area78210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.3, 123.3, 110.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
DetailsThe biological assembly is a homo-octamer generated by crystallographic symmetry

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Components

#1: Protein 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE / Biphenyl-2 / 3-diol 1 / 2-dioxygenase / DHBD


Mass: 32377.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400
Description: HYPEREXPRESSED IN THE PARENT STRAIN. (This organism has been reclassified. Prior publications may refer to this source as Pseudomonas sp. strain LB400.)
Gene: BPHC / Plasmid: PLEBD4 / Production host: Burkholderia cepacia (bacteria)
References: UniProt: P47228, biphenyl-2,3-diol 1,2-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-BPY / BIPHENYL-2,3-DIOL


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2
#4: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.22 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, t-butanol, 2,3-dihydroxybiphenyl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 21, 1995 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 28856 / Num. obs: 28856 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 34.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 5 / Num. unique all: 2728 / % possible all: 95.2
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.63

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HAN

1han


Resolution: 2→7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: All Fe-ligand bond distances were harmonically restrained to an equilibrium distance of 2.2 Angstroms using a weak force constant of 10 kcal/(mole x Angstrom-squared). Bond length, bond ...Details: All Fe-ligand bond distances were harmonically restrained to an equilibrium distance of 2.2 Angstroms using a weak force constant of 10 kcal/(mole x Angstrom-squared). Bond length, bond angle, and planarity restraints similar to those used for aromatic side chains were applied to het group BPY. The torsion angle between the rings of BPY was unrestrained.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1663 -RANDOM
Rwork0.163 ---
all0.203 28098 --
obs0.198 28098 98 %-
Displacement parametersBiso mean: 21.3 Å2
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 20 115 2351
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.488
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_dihedral_angle_d24.464
X-RAY DIFFRACTIONx_improper_angle_d1.341
X-RAY DIFFRACTIONx_mcbond_it21
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it2.71
X-RAY DIFFRACTIONx_scangle_it1.5
LS refinement shellResolution: 2→2.03 Å
RfactorNum. reflection% reflection
Rfree0.25 62 -
Rwork0.238 --
obs-941 89.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 7 Å / Num. reflection obs: 26435 / σ(F): 0 / Rfactor obs: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.464
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.341
X-RAY DIFFRACTIONx_mcbond_it21.5
X-RAY DIFFRACTIONx_scbond_it2.72
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.25 / Num. reflection Rfree: 62 / Rfactor Rwork: 0.238

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