[English] 日本語
Yorodumi
- PDB-5exe: Crystal structure of oxalate oxidoreductase from Moorella thermoa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5exe
TitleCrystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-TPP adduct
Components(Oxalate oxidoreductase subunit ...) x 3
KeywordsOXIDOREDUCTASE / oxalate / OFOR / thiamine
Function / homology
Function and homology information


oxalate oxidoreductase / oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / oxalate catabolic process / thiamine pyrophosphate binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / metal ion binding
Similarity search - Function
: / : / : / 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / : / Pyruvate-ferredoxin Oxidoreductase; domain 3 / Pyruvate-ferredoxin oxidoreductase, PFOR, domain III / Pyruvate:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain ...: / : / : / 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / : / Pyruvate-ferredoxin Oxidoreductase; domain 3 / Pyruvate-ferredoxin oxidoreductase, PFOR, domain III / Pyruvate:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain / : / Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg / Pyruvate-flavodoxin oxidoreductase, central domain / Pyruvate/ketoisovalerate oxidoreductase, catalytic domain / Pyruvate ferredoxin/flavodoxin oxidoreductase / Rossmann fold - #920 / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5SR / IRON/SULFUR CLUSTER / Oxalate oxidoreductase subunit delta / Oxalate oxidoreductase subunit alpha / Oxalate oxidoreductase subunit beta
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsGibson, M.I. / Chen, P.Y.-T. / Drennan, C.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography.
Authors: Gibson, M.I. / Chen, P.Y. / Johnson, A.C. / Pierce, E. / Can, M. / Ragsdale, S.W. / Drennan, C.L.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Data collection
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oxalate oxidoreductase subunit alpha
B: Oxalate oxidoreductase subunit delta
C: Oxalate oxidoreductase subunit beta
D: Oxalate oxidoreductase subunit alpha
E: Oxalate oxidoreductase subunit delta
F: Oxalate oxidoreductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,09418
Polymers223,9526
Non-polymers3,14212
Water43,8122432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36130 Å2
ΔGint-337 kcal/mol
Surface area58460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.653, 144.131, 161.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Oxalate oxidoreductase subunit ... , 3 types, 6 molecules ADBECF

#1: Protein Oxalate oxidoreductase subunit alpha / OOR subunit alpha


Mass: 43737.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Moorella thermoacetica (strain ATCC 39073) (bacteria)
Strain: ATCC 39073 / References: UniProt: Q2RI41, oxalate oxidoreductase
#2: Protein Oxalate oxidoreductase subunit delta / OOR delta subunit


Mass: 33960.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Moorella thermoacetica (strain ATCC 39073) (bacteria)
Strain: ATCC 39073 / References: UniProt: Q2RI40, oxalate oxidoreductase
#3: Protein Oxalate oxidoreductase subunit beta / OOR subunit beta


Mass: 34277.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Moorella thermoacetica (strain ATCC 39073) (bacteria)
Strain: ATCC 39073 / References: UniProt: Q2RI42, oxalate oxidoreductase

-
Non-polymers , 5 types, 2444 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-5SR / [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-carboxy-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 468.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N4O9P2S
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2432 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals were grown in a Coy anaerobic chamber under an Ar/H2 gas mixture. OOR was mixed with the well solution containing PEG 3000 and Tacsimate (pH 7.0), in drops composed of 1 uL well ...Details: Crystals were grown in a Coy anaerobic chamber under an Ar/H2 gas mixture. OOR was mixed with the well solution containing PEG 3000 and Tacsimate (pH 7.0), in drops composed of 1 uL well solution and 1 uL OOR (30 mg/ml) with the addition of 0.2 uL of 100 mM oxalic acid (pH 8.0) to the crystallization drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 200377 / % possible obs: 94.4 % / Redundancy: 5.9 % / Rsym value: 0.129 / Net I/σ(I): 7.7
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.9 / % possible all: 75

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
Cootmodel building
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C4I

5c4i


Resolution: 1.88→48.704 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 10067 5.03 %
Rwork0.1814 --
obs0.183 200261 92.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→48.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15461 0 110 2432 18003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616341
X-RAY DIFFRACTIONf_angle_d1.00222254
X-RAY DIFFRACTIONf_dihedral_angle_d13.4966040
X-RAY DIFFRACTIONf_chiral_restr0.0362436
X-RAY DIFFRACTIONf_plane_restr0.0062895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8786-1.89990.33871570.28823003X-RAY DIFFRACTION44
1.8999-1.92230.32812740.31065030X-RAY DIFFRACTION75
1.9223-1.94570.31512720.29185252X-RAY DIFFRACTION78
1.9457-1.97030.28962720.28865391X-RAY DIFFRACTION79
1.9703-1.99630.28932920.28715526X-RAY DIFFRACTION82
1.9963-2.02360.322850.27535669X-RAY DIFFRACTION83
2.0236-2.05250.29943110.26515773X-RAY DIFFRACTION86
2.0525-2.08320.28613440.25346050X-RAY DIFFRACTION89
2.0832-2.11570.29383090.2536299X-RAY DIFFRACTION93
2.1157-2.15040.2633450.24216523X-RAY DIFFRACTION96
2.1504-2.18750.25633480.23136649X-RAY DIFFRACTION98
2.1875-2.22730.26333790.22756666X-RAY DIFFRACTION99
2.2273-2.27010.26163720.21446713X-RAY DIFFRACTION99
2.2701-2.31640.25153660.20696741X-RAY DIFFRACTION100
2.3164-2.36680.23883240.19476767X-RAY DIFFRACTION99
2.3668-2.42180.22563570.1876762X-RAY DIFFRACTION99
2.4218-2.48240.22383530.1886671X-RAY DIFFRACTION98
2.4824-2.54950.24083960.1856634X-RAY DIFFRACTION98
2.5495-2.62450.21273900.17496765X-RAY DIFFRACTION99
2.6245-2.70920.21093650.17416787X-RAY DIFFRACTION100
2.7092-2.80610.21213430.17556778X-RAY DIFFRACTION100
2.8061-2.91840.20063480.176828X-RAY DIFFRACTION100
2.9184-3.05120.21223490.17116860X-RAY DIFFRACTION100
3.0512-3.2120.18963580.16456728X-RAY DIFFRACTION98
3.212-3.41320.20243090.16086786X-RAY DIFFRACTION98
3.4132-3.67670.17933800.15416842X-RAY DIFFRACTION99
3.6767-4.04650.16983760.13646853X-RAY DIFFRACTION100
4.0465-4.63170.16313640.12946887X-RAY DIFFRACTION99
4.6317-5.83390.15653520.14226848X-RAY DIFFRACTION98
5.8339-48.72080.19173770.17477113X-RAY DIFFRACTION98

+
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