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- PDB-1han: CRYSTAL STRUCTURE OF THE BIPHENYL-CLEAVING EXTRADIOL DIOXYGENASE ... -

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Basic information

Entry
Database: PDB / ID: 1han
TitleCRYSTAL STRUCTURE OF THE BIPHENYL-CLEAVING EXTRADIOL DIOXYGENASE FROM A PCB-DEGRADING PSEUDOMONAD
Components2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE (OXYGENASE) / EXTRADIOL DIOXYGENASE
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
: / TERTIARY-BUTYL ALCOHOL / Biphenyl-2,3-diol 1,2-dioxygenase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHan, S. / Bolin, J.T.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Purification and Crystallization of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase
Authors: Eltis, L.D. / Hofmann, B. / Hecht, H.-J. / Lunsdorf, H. / Timmis, K.N.
History
DepositionAug 30, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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
Remark 650HELIX HELIX DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED IN PROCHECK WITH CONFIRMATION ...HELIX HELIX DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED IN PROCHECK WITH CONFIRMATION AND MODIFICATION BY VISUAL INSPECTION.
Remark 700SHEET SHEET DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED IN PROCHECK WITH CONFIRMATION ...SHEET SHEET DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED IN PROCHECK WITH CONFIRMATION AND MODIFICATION BY VISUAL INSPECTION. SHEET_ID: N; STRANDS ARE LABELED F,G,H,E,A,D,C,B IN PUBLICATIONS. SHEET_ID: C; STRANDS ARE LABELED R,N,O,P,M,I,L,K,J,Q IN PUBLICATIONS.

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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)32,5634
Polymers32,3781
Non-polymers1863
Water2,504139
1
A: 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)260,50732
Polymers259,0218
Non-polymers1,48624
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 area21590 Å2
ΔGint-237 kcal/mol
Surface area79080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.580, 122.580, 111.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 2 .. 8038 THE ENZYME IS AN OCTAMER IN SOLUTION. THE DISTRIBUTED COORDINATES ARE FOR A MONOMER BELONGING TO AN OCTAMER AT FRACTIONAL COORDINATES (0.0,0.0,0.5), WHICH IS A SITE OF 422 (D4) POINT SYMMETRY. APPLY THE FOLLOWING SEVEN OPERATIONS TO ALL ATOMS IN THIS ENTRY TO GENERATE THE OTHER SUBUNITS IN THIS OCTAMER. SYMMETRY1 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 1 -1.000000 0.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 2 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 3 0.000000 -1.000000 0.000000 0.00000 SYMMETRY2 3 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 3 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 4 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 4 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 4 0.000000 0.000000 -1.000000 111.36000 SYMMETRY1 5 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 5 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 5 0.000000 0.000000 -1.000000 111.36000 SYMMETRY1 6 0.000000 -1.000000 0.000000 0.00000 SYMMETRY2 6 -1.000000 0.000000 0.000000 0.00000 SYMMETRY3 6 0.000000 0.000000 -1.000000 111.36000 SYMMETRY1 7 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 7 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 7 0.000000 0.000000 -1.000000 111.36000

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Components

#1: Protein 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE / BIPHENYL-2 / 3-DIOL 1 / 2-DIOXYGENASE / DHBD / BPHC


Mass: 32377.598 Da / Num. of mol.: 1 / Mutation: WILD-TYPE
Source method: isolated from a genetically manipulated source
Details: FE(II) FORM UNDER ANAEROBIC CONDITIONS / Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Description: HYPEREXPRESSED IN THE PARENT STRAIN / Gene: BPHC / Plasmid: PLEBD4 / Gene (production host): BPHC / Production host: Burkholderia cepacia (bacteria)
References: UniProt: P47228, biphenyl-2,3-diol 1,2-dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUE 501 IS AN ADVENTITIOUS FE ATOM PRESENT WITH PARTIAL OCCUPANCY ONLY WHEN THE CRYSTAL ...RESIDUE 501 IS AN ADVENTITIOUS FE ATOM PRESENT WITH PARTIAL OCCUPANCY ONLY WHEN THE CRYSTAL STABILIZING SOLUTION CONTAINS EXCESS FERROUS AMMONIUM SULFATE. RESIDUE 600 IS A T-BUTANOL MOLECULE ASSIGNED TO AN APPROPRIATE DENSITY FEATURE. T-BUTANOL IS INCLUDED AT BETWEEN 10-15% IN ALL CRYSTAL GROWTH AND STABILIZING SOLUTIONS. THE T-BUTANOL IS APPARENTLY ROTATIONALLY DISORDERED AND THUS THE POSITION OF THE HYDROXYL OXYGEN AND METHYL CARBONS ARE NOT WELL-DETERMINED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.91 %
Description: MWPC DATA WERE USED IN STRUCTURE DETERMINATION AND INITIAL REFINEMENT. IMAGING PLATE DATA WERE USED IN FINAL REFINEMENT. REDUNDANCY AND MERGING R STATISTICS CITED ABOVE ARE FOR IMAGING ...Description: MWPC DATA WERE USED IN STRUCTURE DETERMINATION AND INITIAL REFINEMENT. IMAGING PLATE DATA WERE USED IN FINAL REFINEMENT. REDUNDANCY AND MERGING R STATISTICS CITED ABOVE ARE FOR IMAGING PLATE DATA FROM ONE CRYSTAL.
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 5-10 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-22 %PEG40001reservoir
210-15 %t-butanol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12901
21
Diffraction source
IDWavelength
11.542
21.542
Detector
TypeIDDetectorDate
XUONG-HAMLIN MULTIWIRE1AREA DETECTORJul 1, 1993
RIGAKU RAXIS II2IMAGE PLATEDec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 33261 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.06
Reflection shellHighest resolution: 1.9 Å / Redundancy: 4.2 %
Reflection
*PLUS
Observed criterion σ(I): 3 / Num. measured all: 287451 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Num. unique obs: 3303 / Num. measured obs: 13817 / Rmerge(I) obs: 0.225

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
HKL(DENZO)data reduction
X-PLOR3.1phasing
RefinementResolution: 1.9→7 Å / σ(F): 1
Details: THE SIDE CHAIN OF MET 246 IS NEAR THE ACTIVE SITE FE AND IS DISORDERED BETWEEN TWO MAJOR CONFORMERS. THE ELECTRON DENSITY MAPS SUGGEST THAT SEVERAL ADDITIONAL RESIDUES HAVE TWO OF MORE ...Details: THE SIDE CHAIN OF MET 246 IS NEAR THE ACTIVE SITE FE AND IS DISORDERED BETWEEN TWO MAJOR CONFORMERS. THE ELECTRON DENSITY MAPS SUGGEST THAT SEVERAL ADDITIONAL RESIDUES HAVE TWO OF MORE CONFORMATIONS. IN ALL CASES ONLY ONE CONFORMATION WAS REFINED. SEVERAL SIDE CHAIN ATOMS HAVE BEEN ASSIGNED OCCUPANCIES OF 0.10 TO INDICATE THE PRESENCE OF POOR DENSITY AND UNRELIABLE COORDINATES. THESE OCCUPANCIES WERE NOT REFINED. THE OCCUPANCY OF THE FE(II) ION INCLUDED AS RESIDUE 501 WAS ASSIGNED A VALUE OF 0.5 BASED ON ITS RELATIVE ANOMALOUS DIFFERENCE DENSITY. THIS OCCUPANCY WAS NOT REFINED.
RfactorNum. reflection% reflection
Rfree0.19 -5.9 %
Rwork0.162 --
obs0.162 29672 93.2 %
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 7 139 2352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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