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

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Basic information

Entry
Database: PDB / ID: 1knd
TitleCrystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with Catechol under Anaerobic Condition
Components2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE / dioxygenase / 2 / 3-dihydroxybiphenyl / catechol
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
CATECHOL / : / TERTIARY-BUTYL ALCOHOL / Biphenyl-2,3-diol 1,2-dioxygenase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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: 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.
#2: Journal: Handbook of Metalloproteins / Year: 2001
Title: 2,3-Dihydroxybiphenyl 1,2-dioxygenase.
Authors: Bolin, J.T. / Eltis, L.D.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)32,7486
Polymers32,3781
Non-polymers3705
Water2,180121
1
A: 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)261,98148
Polymers259,0218
Non-polymers2,96040
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 area26350 Å2
ΔGint-157 kcal/mol
Surface area77950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.8, 122.8, 110.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
DetailsBiological assembly is 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.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O2
#4: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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, catechol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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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 23, 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: 1.9→30 Å / Num. all: 32091 / Num. obs: 32091 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rsym value: 0.061 / Net I/σ(I): 44.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 2397 / Rsym value: 0.27 / % possible all: 73.1

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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: 1.9→7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: ALL FE-PROTEIN 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-PROTEIN 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 CAQ (CATECHOL). FE-CAQ AND FE-WATER BOND DISTANCES WERE NOT RESTRAINED. THE REFINED MODEL INCLUDES TWO MUTALLY EXCLUSIVE STRUCTURES IN THE VICINITY OF THE ACTIVE SITE. STRUCTURE ONE (labeled with alternate conformation marker A) INCLUDES THE SUBSTRATE CATECHOL (CAQ 301) AND WATERS 9001 and 9002 AT 50% OCCUPANCY. ATOMS O3 AND O4 OF CAQ 301 AND WATER 9001 ARE COORDINATED TO FE2 500. STRUCTURE TWO (labeled with alternate conformation marker B) INCLUDES ONE MOLECULE OF T-BUTANOL (TBU 600) AND WATERS 3001, 3012, AND 4014 AT 50% OCCUPANCY, AND IS EQUIVALENT TO THE SUBSTRATE-FREE STRUCTURE WHERE WATERS 3001 AND 3012 ARE COORDINATED TO FE2 500.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1797 -RANDOM
Rwork0.164 ---
all0.201 ---
obs0.198 30189 89.4 %-
Displacement parametersBiso mean: 23.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 20 121 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_mcbond_it21
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it2.91
X-RAY DIFFRACTIONx_scangle_it1.5
LS refinement shellResolution: 1.9→1.93 Å
RfactorNum. reflection% reflection
Rfree0.2996 44 -
Rwork0.2292 --
obs-698 89.4 %

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