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- PDB-2xr8: Crystal structure of biphenyl dioxygenase from Burkholderia xenov... -

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Basic information

Entry
Database: PDB / ID: 2xr8
TitleCrystal structure of biphenyl dioxygenase from Burkholderia xenovorans LB400
Components
  • BIPHENYL DIOXYGENASE SUBUNIT ALPHA
  • BIPHENYL DIOXYGENASE SUBUNIT BETA
KeywordsOXIDOREDUCTASE / DEGRADATION / BPDO
Function / homology
Function and homology information


biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / aromatic compound catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Nuclear Transport Factor 2; Chain: A, - #50 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Biphenyl dioxygenase subunit alpha / Biphenyl dioxygenase subunit beta
Similarity search - Component
Biological speciesBURKHOLDERIA XENOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsKumar, P. / Bolin, J.T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Insight Into the Expanded Pcb-Degrading Abilities of a Biphenyl Dioxygenase Obtained by Directed Evolution.
Authors: Kumar, P. / Mohammadi, M. / Viger, J.F. / Barriault, D. / Gomez-Gil, L. / Eltis, L.D. / Bolin, J.T. / Sylvestre, M.
History
DepositionSep 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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 DIOXYGENASE SUBUNIT ALPHA
B: BIPHENYL DIOXYGENASE SUBUNIT BETA
C: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
D: BIPHENYL DIOXYGENASE SUBUNIT BETA
E: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
F: BIPHENYL DIOXYGENASE SUBUNIT BETA
G: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
H: BIPHENYL DIOXYGENASE SUBUNIT BETA
I: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
J: BIPHENYL DIOXYGENASE SUBUNIT BETA
K: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
L: BIPHENYL DIOXYGENASE SUBUNIT BETA
M: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
N: BIPHENYL DIOXYGENASE SUBUNIT BETA
O: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
P: BIPHENYL DIOXYGENASE SUBUNIT BETA
Q: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
R: BIPHENYL DIOXYGENASE SUBUNIT BETA
S: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
T: BIPHENYL DIOXYGENASE SUBUNIT BETA
U: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
V: BIPHENYL DIOXYGENASE SUBUNIT BETA
W: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
X: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)887,03948
Polymers884,25924
Non-polymers2,78024
Water12,466692
1
A: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
B: BIPHENYL DIOXYGENASE SUBUNIT BETA
C: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
D: BIPHENYL DIOXYGENASE SUBUNIT BETA
E: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
F: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,76012
Polymers221,0656
Non-polymers6956
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32630 Å2
ΔGint-183 kcal/mol
Surface area56390 Å2
MethodPISA
2
G: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
H: BIPHENYL DIOXYGENASE SUBUNIT BETA
I: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
J: BIPHENYL DIOXYGENASE SUBUNIT BETA
K: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
L: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,76012
Polymers221,0656
Non-polymers6956
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32670 Å2
ΔGint-185.5 kcal/mol
Surface area56560 Å2
MethodPISA
3
S: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
T: BIPHENYL DIOXYGENASE SUBUNIT BETA
U: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
V: BIPHENYL DIOXYGENASE SUBUNIT BETA
W: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
X: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,76012
Polymers221,0656
Non-polymers6956
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32730 Å2
ΔGint-183 kcal/mol
Surface area56060 Å2
MethodPISA
4
M: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
N: BIPHENYL DIOXYGENASE SUBUNIT BETA
O: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
P: BIPHENYL DIOXYGENASE SUBUNIT BETA
Q: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
R: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,76012
Polymers221,0656
Non-polymers6956
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32430 Å2
ΔGint-183.8 kcal/mol
Surface area58920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.585, 132.350, 132.984
Angle α, β, γ (deg.)102.60, 102.68, 104.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
BIPHENYL DIOXYGENASE SUBUNIT ALPHA / BIPHENYL 2 / 3-DIOXYGENASE / SUBUNIT A


Mass: 51574.383 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37333, biphenyl 2,3-dioxygenase
#2: Protein
BIPHENYL DIOXYGENASE SUBUNIT BETA / BIPHENYL 2 / 3-DIOXYGENASE / SUBUNIT B


Mass: 22113.846 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37334, biphenyl 2,3-dioxygenase
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 6 / Details: pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1
DetectorType: ADSC SX-165 / Detector: CCD / Date: Jul 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→120 Å / Num. obs: 255418 / % possible obs: 89 % / Observed criterion σ(I): 1.4 / Redundancy: 2.8 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.8
Reflection shellResolution: 2.49→2.6 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.4 / % possible all: 30

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GZY

3gzy


Resolution: 2.49→129.1 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.873 / SU B: 18.294 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 1.122 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26714 753 0.3 %RANDOM
Rwork0.21633 ---
obs0.21649 254621 89.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.197 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.11 Å20.56 Å2
2---0.23 Å20.28 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.49→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59172 0 60 692 59924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02260864
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.93482497
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27257320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83623.3013117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.936159846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.51215504
X-RAY DIFFRACTIONr_chiral_restr0.0630.28460
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0247724
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1640.227216
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.240707
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.22547
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2381.537598
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.372258593
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.46327073
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7494.523880
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 11 -
Rwork0.37 5460 -
obs--25.94 %

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