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- PDB-1lgt: CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD)... -

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Basic information

Entry
Database: PDB / ID: 1lgt
TitleCRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2'-Cl DIHYDROXYBIPHENYL (DHB)
ComponentsBIPHENYL-2,3-DIOL 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE / Extradiol dioxygenase / 2 / 3-dihydroxybiphenyl / Non-heme iron / Anaerobic / PCB biodegradation
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
2'-CHLORO-BIPHENYL-2,3-DIOL / : / Biphenyl-2,3-diol 1,2-dioxygenase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDai, S. / Bolin, J.T.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Identification and analysis of a bottleneck in PCB biodegradation
Authors: Dai, S. / Vaillancourt, F.H. / Maaroufi, H. / Drouin, N.M. / Neau, D.B. / Snieckus, V. / Bolin, J.T. / Eltis, L.D.
History
DepositionApr 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,9315
Polymers32,3781
Non-polymers5534
Water5,837324
1
A: BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)263,44540
Polymers259,0218
Non-polymers4,42432
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 area26340 Å2
ΔGint-450 kcal/mol
Surface area78480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.337, 122.337, 106.947
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 BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE / 23OHBP oxygenase / 2 / 3-dihydroxybiphenyl 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: Burkholderia sp. strain LB400 has been reclassifed. Prior publications may refer to this organism as pseudomonas sp. strain LB400 or burkholderia cepacia strain LB400. See M.G.FAIN,J.D. ...Description: Burkholderia sp. strain LB400 has been reclassifed. Prior publications may refer to this organism as pseudomonas sp. strain LB400 or burkholderia cepacia strain LB400. See M.G.FAIN,J.D.HADDOCK, CURRENT MICROBIOL. (2001) 42:269-73
Plasmid: pLEBD4 / Production host: Pseudomonas putida (bacteria) / Strain (production host): KT2442
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-BP3 / 2'-CHLORO-BIPHENYL-2,3-DIOL


Mass: 220.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9ClO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, t-Butanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 5-10 ℃ / Method: vapor diffusion / Details: Han, S., (1995) Science, 270, 976.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-22 %PEG40001reservoir
210-15 %t-butanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97833 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 10, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97833 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. all: 84926 / Num. obs: 84926 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.34 / % possible all: 96.7
Reflection
*PLUS
Num. obs: 44042 / % possible obs: 96.8 % / Num. measured all: 1480972
Reflection shell
*PLUS
% possible obs: 94.8 % / Rmerge(I) obs: 0.34

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2522232.85 / Data cutoff high rms absF: 2522232.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Solvents 8036, 9204 and 9206 mark density features that may be associated with a partially occupied PEG molecule from the crystallization.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2170 5 %RANDOM
Rwork0.207 ---
all-43300 --
obs-43300 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.2451 Å2 / ksol: 0.391747 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20 Å2
2---1.48 Å20 Å2
3---2.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 32 324 2561
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1581.5
X-RAY DIFFRACTIONc_mcangle_it1.8562
X-RAY DIFFRACTIONc_scbond_it1.7982
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 406 5.6 %
Rwork0.283 6844 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPOLOGY_INFILE_1
X-RAY DIFFRACTION2PARAMETER_INFILE_2TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3WATER_REP.PARAMTOPOLOGY_INFILE_3
X-RAY DIFFRACTION4BP3.PARTOPOLOGY_INFILE_4
X-RAY DIFFRACTION5ION.PARAMTOPOLOGY_INFILE_5
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0063
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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