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

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Basic information

Entry
Database: PDB / ID: 1knf
TitleCrystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition
Components2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE / dioxygenase / 2 / 3-dihydroxybiphenyl / 3-methyl 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 / 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 ...2,3-dihydroxybiphenyl 1,2-dioxygenase / 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
: / 3-METHYLCATECHOL / 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_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.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

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)32,7626
Polymers32,3781
Non-polymers3845
Water2,180121
1
A: 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)262,09348
Polymers259,0218
Non-polymers3,07340
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 area26660 Å2
ΔGint-215 kcal/mol
Surface area78170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.1, 123.1, 110.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
DetailsThe biological 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-MBD / 3-METHYLCATECHOL / 3-METHYL-BENZENE-1,2-DIOL / 3-Methylcatechol


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2
#4: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#5: Water ChemComp-HOH / water / 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, 3-methyl 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 30, 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→40 Å / Num. all: 32641 / Num. obs: 32641 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.08 / Net I/σ(I): 44.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / 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 A SUBSTRATE 3-METHYL-CATECHOL (MBD 301) AND WATERS 9001 and 9002 AT 50% OCCUPANCY. ATOMS OA1 AND OA2 OF MBD 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
Rfree0.195 1811 -RANDOM
Rwork0.168 ---
all0.207 30504 --
obs0.199 30504 97 %-
Displacement parametersBiso mean: 24.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 21 121 2358
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.47
X-RAY DIFFRACTIONx_mcbond_it1.91
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it2.81
X-RAY DIFFRACTIONx_scangle_it1.5
LS refinement shellResolution: 1.9→1.93 Å
RfactorNum. reflection% reflection
Rfree0.298 46 -
Rwork0.273 --
obs-767 81.9 %

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