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- PDB-2yfj: Crystal structure of Biphenyl dioxygenase variant RR41 with diben... -

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Basic information

Entry
Database: PDB / ID: 2yfj
TitleCrystal structure of Biphenyl dioxygenase variant RR41 with dibenzofuran
Components(BIPHENYL DIOXYGENASE SUBUNIT ...) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / 3-phenylpropionate catabolic process / 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] domain / Rieske [2Fe-2S] iron-sulphur 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
DIBENZOFURAN / : / 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: 2.15 Å
AuthorsKumar, P. / Sylvestre, M. / Bolin, J.T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Retuning Rieske-Type Oxygenases to Expand Substrate Range.
Authors: Mohammadi, M. / Viger, J. / Kumar, P. / Barriault, D. / Bolin, J.T. / Sylvestre, M.
History
DepositionApr 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Version format compliance
Revision 1.2Dec 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,95227
Polymers442,05712
Non-polymers1,89515
Water11,746652
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)222,22815
Polymers221,0296
Non-polymers1,2009
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32690 Å2
ΔGint-189.1 kcal/mol
Surface area55800 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)221,72412
Polymers221,0296
Non-polymers6956
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33050 Å2
ΔGint-189.3 kcal/mol
Surface area56380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.979, 278.125, 92.956
Angle α, β, γ (deg.)90.00, 117.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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BIPHENYL DIOXYGENASE SUBUNIT ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
BIPHENYL DIOXYGENASE SUBUNIT ALPHA / BIPHENYL DIOXYGENASE VARIANT RR41 ALPHA SUBUNIT / BIPHENYL 2\ / 3-DIOXYGENASE


Mass: 51562.398 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Variant: RR41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P37333, biphenyl 2,3-dioxygenase
#2: Protein
BIPHENYL DIOXYGENASE SUBUNIT BETA / BIPHENYL DIOXYGENASE VARIANT RR41 BETA / BIPHENYL 2\ / 3-DIOXYGENASE


Mass: 22113.846 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Variant: RR41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P37334, biphenyl 2,3-dioxygenase

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Non-polymers , 4 types, 667 molecules

#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-1IT / DIBENZOFURAN


Mass: 168.191 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN A, PHE 336 TO MET ...ENGINEERED RESIDUE IN CHAIN A, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN A, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN A, ASN 338 TO GLN ENGINEERED RESIDUE IN CHAIN A, ILE 341 TO VAL ENGINEERED RESIDUE IN CHAIN A, LEU 409 TO PHE ENGINEERED RESIDUE IN CHAIN C, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN C, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN C, ASN 338 TO GLN ENGINEERED RESIDUE IN CHAIN C, ILE 341 TO VAL ENGINEERED RESIDUE IN CHAIN C, LEU 409 TO PHE ENGINEERED RESIDUE IN CHAIN E, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN E, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN E, ASN 338 TO GLN ENGINEERED RESIDUE IN CHAIN E, ILE 341 TO VAL ENGINEERED RESIDUE IN CHAIN E, LEU 409 TO PHE ENGINEERED RESIDUE IN CHAIN G, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN G, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN G, ASN 338 TO GLN ENGINEERED RESIDUE IN CHAIN G, ILE 341 TO VAL ENGINEERED RESIDUE IN CHAIN G, LEU 409 TO PHE ENGINEERED RESIDUE IN CHAIN I, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN I, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN I, ASN 338 TO GLN ENGINEERED RESIDUE IN CHAIN I, ILE 341 TO VAL ENGINEERED RESIDUE IN CHAIN I, LEU 409 TO PHE ENGINEERED RESIDUE IN CHAIN K, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN K, PHE 336 TO MET ENGINEERED RESIDUE IN CHAIN K, ASN 338 TO GLN ENGINEERED RESIDUE IN CHAIN K, ILE 341 TO VAL ENGINEERED RESIDUE IN CHAIN K, LEU 409 TO PHE

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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 6 / Details: PEG 5000 MME AND PIPES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Jul 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 210175 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.02
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XR8

2xr8


Resolution: 2.15→138.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.747 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23312 9876 5 %RANDOM
Rwork0.2036 ---
obs0.20509 186884 92.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.576 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20.52 Å2
2---0.68 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.15→138.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29556 0 69 652 30277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02130447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.921.93541271
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.99553660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88123.3081560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.239154902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.53715252
X-RAY DIFFRACTIONr_chiral_restr0.0590.24218
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0223907
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1520.213172
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.220430
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.21499
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1410.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.2275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.265
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.171.518874
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.302229280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.385313615
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6274.511979
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: 2.148→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 647 -
Rwork0.276 12038 -
obs--80.89 %

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