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

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Basic information

Entry
Database: PDB / ID: 1lkd
TitleCRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL 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',6'-DICHLORO-BIPHENYL-2,6-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 24, 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)33,2826
Polymers32,3781
Non-polymers9045
Water5,873326
1
A: BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)266,25548
Polymers259,0218
Non-polymers7,23440
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 area31700 Å2
ΔGint-526 kcal/mol
Surface area76880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.640, 122.640, 107.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-9236-

HOH

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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-BP6 / 2',6'-DICHLORO-BIPHENYL-2,6-DIOL


Mass: 255.097 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H8Cl2O2
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, t-Butanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
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 (III) / 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: 46029 / Num. obs: 46029 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.409 / % possible all: 73.7
Reflection
*PLUS
Num. measured all: 2212442
Reflection shell
*PLUS
% possible obs: 73.7 %

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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→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2808076.19 / Data cutoff high rms absF: 2808076.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2012 5 %RANDOM
Rwork0.203 ---
all-40229 --
obs-40229 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.3977 Å2 / ksol: 0.413408 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.38 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 53 326 2584
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.3441.5
X-RAY DIFFRACTIONc_mcangle_it2.1752
X-RAY DIFFRACTIONc_scbond_it2.1572
X-RAY DIFFRACTIONc_scangle_it3.322.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 282 5.2 %
Rwork0.298 5184 -
obs--73.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPOLOGY_INFILE_1
X-RAY DIFFRACTION2PEG.PARTOPOLOGY_INFILE_2
X-RAY DIFFRACTION3WATER_REP.PARAMTOPOLOGY_INFILE_3
X-RAY DIFFRACTION4BP6.PARTOPOLOGY_INFILE_4
X-RAY DIFFRACTION5ION.PARAMTOPOLOGY_INFILE_5
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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