[English] 日本語
Yorodumi
- PDB-2yfi: Crystal Structure of Biphenyl dioxygenase variant RR41 (BPDO-RR41) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yfi
TitleCrystal Structure of Biphenyl dioxygenase variant RR41 (BPDO-RR41)
Components
  • BIPHENYL DIOXYGENASE SUBUNIT ALPHA
  • BIPHENYL DIOXYGENASE SUBUNIT BETA
KeywordsOXIDOREDUCTASE / DEGRADATION
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
: / 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. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)443,44724
Polymers442,05712
Non-polymers1,39012
Water21,8521213
1
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 area32830 Å2
ΔGint-191.2 kcal/mol
Surface area56690 Å2
MethodPISA
2
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)221,72412
Polymers221,0296
Non-polymers6956
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32530 Å2
ΔGint-183.7 kcal/mol
Surface area56170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.969, 277.808, 92.933
Angle α, β, γ (deg.)90.00, 117.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
BIPHENYL DIOXYGENASE SUBUNIT ALPHA / 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 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1213 / Source method: isolated from a natural source / Formula: H2O
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 6 / Details: PEG 5000 MME AND PIPES PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. obs: 208106 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / % possible all: 94

-
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: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.261 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23163 10445 5 %RANDOM
Rwork0.19992 ---
obs0.20152 197600 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å21.12 Å2
2---0.07 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.15→138.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29556 0 30 1213 30799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02130402
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8811.93341208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.06853660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81523.3081560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.329154902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.55115252
X-RAY DIFFRACTIONr_chiral_restr0.060.24218
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0223868
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1520.213604
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.220396
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.21930
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.2268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.277
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1831.518862
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.325229280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.419313501
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6934.511916
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: 2.153→2.209 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 729 -
Rwork0.277 13558 -
obs--92.19 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more