[English] 日本語
Yorodumi
- PDB-5c4i: Structure of an Oxalate Oxidoreductase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c4i
TitleStructure of an Oxalate Oxidoreductase
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 / metal ion binding
Similarity search - Function
2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / 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 / 4Fe-4S binding domain ...2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / 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 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / THIAMINE DIPHOSPHATE / Oxalate oxidoreductase subunit delta / Oxalate oxidoreductase subunit alpha / Oxalate oxidoreductase subunit beta
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.274 Å
AuthorsGibson, M.I. / Brignole, E.J. / Pierce, E. / Can, M. / Ragsdale, S.W. / Drennan, C.L.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM39451 United States
National Science Foundation (NSF, United States)1122374 United States
Howard Hughes Medical Institute (HHMI) United States
Martin 592 Family Society of Fellows for Sustainability United States
CitationJournal: Biochemistry / Year: 2015
Title: The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism.
Authors: Gibson, M.I. / Brignole, E.J. / Pierce, E. / Can, M. / Ragsdale, S.W. / Drennan, C.L.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Mar 16, 2016Group: Data collection
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _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)227,00718
Polymers223,9526
Non-polymers3,05512
Water29,4731636
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39290 Å2
ΔGint-386 kcal/mol
Surface area57000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.351, 152.203, 171.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 (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, 1648 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1636 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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).
PH range: 7.0-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97959 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 82345 / % possible obs: 81.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.076 / Rrim(I) all: 0.188 / Χ2: 1.075 / Net I/av σ(I): 7.958 / Net I/σ(I): 5.4 / Num. measured all: 457689
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.28-2.324.40.57725510.7880.2770.6441.0350.8
2.32-2.364.90.53728030.7890.2510.5961.07256.1
2.36-2.414.90.49929510.8370.2330.5531.06459.1
2.41-2.4650.47931770.870.2210.531.09662.8
2.46-2.5150.4933010.8470.2270.5431.08166.4
2.51-2.5750.47734770.8310.2220.5291.08769.2
2.57-2.635.10.44836390.8510.2090.4971.09671.9
2.63-2.75.20.41335270.8910.190.4571.11670.2
2.7-2.785.70.4240340.9160.1830.4591.08980
2.78-2.875.80.37741930.9190.1620.4121.09783.4
2.87-2.985.80.32644270.9460.140.3551.11687.9
2.98-3.095.60.28847130.9590.1250.3151.10493
3.09-3.245.60.23748250.9670.1040.261.07295.2
3.24-3.415.50.19448210.9760.0870.2141.06595.3
3.41-3.625.60.16546300.9820.0730.1811.05591.1
3.62-3.960.1450130.9880.060.1521.0598.6
3.9-4.2960.12550620.9890.0540.1361.05498.9
4.29-4.915.90.10650890.9930.0460.1161.04598.5
4.91-6.196.20.10549090.9930.0450.1151.0694.9
6.19-506.10.08252030.9960.0350.0891.07895.8

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.274→48.658 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4131 5.02 %Random selection
Rwork0.1739 78160 --
obs0.1761 82291 80.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.69 Å2 / Biso mean: 22.8585 Å2 / Biso min: 4.16 Å2
Refinement stepCycle: final / Resolution: 2.274→48.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15546 0 104 1636 17286
Biso mean--16.13 29.31 -
Num. residues----2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216052
X-RAY DIFFRACTIONf_angle_d0.67321849
X-RAY DIFFRACTIONf_chiral_restr0.0262403
X-RAY DIFFRACTIONf_plane_restr0.0042834
X-RAY DIFFRACTIONf_dihedral_angle_d12.0775897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.274-2.29990.2734880.21451471155947
2.2999-2.32690.252900.21161719180954
2.3269-2.35530.2856950.2121784187955
2.3553-2.38510.27251110.21711830194158
2.3851-2.41650.28161110.21381936204760
2.4165-2.44960.29431110.2181971208262
2.4496-2.48460.2731040.22172099220365
2.4846-2.52170.31791170.20972125224267
2.5217-2.56110.29561180.19942190230869
2.5611-2.60310.24751170.1952318243572
2.6031-2.6480.25681180.19892303242171
2.648-2.69610.23051200.19412180230068
2.6961-2.7480.28161260.19912484261077
2.748-2.8040.21881410.20362610275181
2.804-2.8650.22021360.19982674281084
2.865-2.93160.23161270.20292752287985
2.9316-3.00490.21321420.19432920306290
3.0049-3.08620.2571400.19682995313593
3.0862-3.1770.23751670.18683063323095
3.177-3.27950.22031650.18523099326496
3.2795-3.39670.21861610.17043105326695
3.3967-3.53260.2081560.16122812296887
3.5326-3.69340.17431880.15783136332498
3.6934-3.8880.18211660.1473223338999
3.888-4.13150.18441840.1453187337199
4.1315-4.45030.17881650.13083274343999
4.4503-4.89780.15991530.13023236338998
4.8978-5.60560.17081700.14773060323092
5.6056-7.0590.19891650.176333233488100
7.059-48.66870.22191790.17543281346094

+
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