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- PDB-1kw6: Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in ... -

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Basic information

Entry
Database: PDB / ID: 1kw6
TitleCrystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 1.45 A resolution
Components2,3-Dihydroxybiphenyl dioxygenase
KeywordsOXIDOREDUCTASE / four time repetitions of the beta-alpha-beta-beta-beta motif
Function / homology
Function and homology information


biphenyl-2,3-diol 1,2-dioxygenase / biphenyl-2,3-diol 1,2-dioxygenase activity / aromatic compound catabolic process / 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
BIPHENYL-2,3-DIOL / : / Biphenyl-2,3-diol 1,2-dioxygenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSato, N. / Uragami, Y. / Nishizaki, T. / Takahashi, Y. / Sazaki, G. / Sugimoto, K. / Nonaka, T. / Masai, E. / Fukuda, M. / Senda, T.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
Authors: Sato, N. / Uragami, Y. / Nishizaki, T. / Takahashi, Y. / Sazaki, G. / Sugimoto, K. / Nonaka, T. / Masai, E. / Fukuda, M. / Senda, T.
History
DepositionJan 28, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: 2,3-Dihydroxybiphenyl dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6305
Polymers32,1521
Non-polymers4784
Water5,260292
1
B: 2,3-Dihydroxybiphenyl dioxygenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)261,04040
Polymers257,2128
Non-polymers3,82732
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area29160 Å2
ΔGint-462 kcal/mol
Surface area73650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.829, 121.829, 109.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsThe biological assembly is a octamer generated from the monomer in the asymmetric unit by the operations:

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Components

#1: Protein 2,3-Dihydroxybiphenyl dioxygenase / BphC / Biphenyl-2 / 3-diol 1 / 2-dioxygenase


Mass: 32151.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: KKS102 / Production host: Escherichia coli (E. coli)
References: UniProt: P17297, 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 285 K / Method: batch / pH: 7.5
Details: Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K
Crystal grow
*PLUS
Temperature: 12 ℃ / Method: batch method / Details: Uragami, Y., (2001) J.Inorg.Biochem., 83, 269.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
2100 mMTris-HCl11
327.7 %satammonium sulfate11
418 %(v/v)hexylene glycol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2000
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→26.08 Å / Num. all: 72458 / Num. obs: 72435 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 7.8
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2 / Rsym value: 0.373 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 87.7 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→87.71 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.076 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17102 3654 5 %RANDOM
Rwork0.163 ---
obs0.1634 68780 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.595 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 31 292 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212337
X-RAY DIFFRACTIONr_bond_other_d0.0010.022093
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9483182
X-RAY DIFFRACTIONr_angle_other_deg2.13534848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9613295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33515387
X-RAY DIFFRACTIONr_chiral_restr0.080.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022630
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02508
X-RAY DIFFRACTIONr_nbd_refined0.2210.3451
X-RAY DIFFRACTIONr_nbd_other0.1980.32008
X-RAY DIFFRACTIONr_nbtor_other0.2210.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.5249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.356
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6540.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5971.51437
X-RAY DIFFRACTIONr_mcangle_it1.12522304
X-RAY DIFFRACTIONr_scbond_it1.6963900
X-RAY DIFFRACTIONr_scangle_it2.7334.5877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free1.46121
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 253
Rwork0.272 4978
Refinement
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 87.7 Å / Rfactor Rfree: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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