[English] 日本語
Yorodumi
- PDB-6n2n: Crystal structure of 2-oxoglutarate:ferredoxin oxidoreductase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n2n
TitleCrystal structure of 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus
Components
  • Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit
  • Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein
KeywordsOXIDOREDUCTASE / thiamine pyrophosphate / [4Fe-4S] cluster / carbon fixation / reductive tricarboxylic acid cycle / rTCA / 2-oxoglutarate:ferredoxin oxidoreductase / electron transfer
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors / oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / small molecule metabolic process / thiamine pyrophosphate binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / metal ion binding
Similarity search - Function
2-oxoacid:acceptor oxidoreductase, beta subunit / Pyruvate ferredoxin oxidoreductase beta subunit, C-terminal / Pyruvate ferredoxin oxidoreductase beta subunit C terminal / 2-oxoacid:acceptor oxidoreductase, alpha subunit / : / 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, beta subunit / Pyruvate ferredoxin oxidoreductase beta subunit, C-terminal / Pyruvate ferredoxin oxidoreductase beta subunit C terminal / 2-oxoacid:acceptor oxidoreductase, alpha subunit / : / 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 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / THIAMINE DIPHOSPHATE / Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein / Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit
Similarity search - Component
Biological speciesMagnetococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.937 Å
AuthorsChen, P.Y.-T. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126982 United States
CitationJournal: Joule / Year: 2019
Title: A reverse TCA cycle 2-oxoacid:ferredoxin oxidoreductase that makes C-C bonds from CO2.
Authors: Chen, P.Y. / Li, B. / Drennan, C.L. / Elliott, S.J.
History
DepositionNov 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein
B: Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit
C: Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein
D: Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,71914
Polymers187,7324
Non-polymers1,98710
Water27,1491507
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23440 Å2
ΔGint-293 kcal/mol
Surface area54620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.282, 123.161, 162.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein


Mass: 62159.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria)
Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_1749 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L8G4
#2: Protein Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit


Mass: 31706.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria)
Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_1750 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L8G5

-
Non-polymers , 5 types, 1517 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C12H19N4O7P2S
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1507 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 14% (w/v) PEG 8000, 0.21-0.28 M (NH4)2SO4, and 0.10 M MES pH 6.5

-
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: Aug 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.937→100 Å / Num. obs: 125663 / % possible obs: 97.6 % / Redundancy: 4 % / Rsym value: 0.106 / Net I/σ(I): 7.7
Reflection shellResolution: 1.937→2.01 Å / Num. unique obs: 11651 / CC1/2: 0.735

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WBX, 5C4I, 3G2E

4wbx

5c4i

3g2e


Resolution: 1.937→98.152 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.71
RfactorNum. reflection% reflection
Rfree0.2049 6279 5 %
Rwork0.168 --
obs0.1698 125566 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.937→98.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13116 0 90 1507 14713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513538
X-RAY DIFFRACTIONf_angle_d0.7118333
X-RAY DIFFRACTIONf_dihedral_angle_d15.1388102
X-RAY DIFFRACTIONf_chiral_restr0.0481979
X-RAY DIFFRACTIONf_plane_restr0.0052390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9367-1.95870.30481680.27013200X-RAY DIFFRACTION78
1.9587-1.98180.29441920.27313639X-RAY DIFFRACTION91
1.9818-2.00590.29842040.24733873X-RAY DIFFRACTION96
2.0059-2.03130.30992090.23163971X-RAY DIFFRACTION99
2.0313-2.05810.26612080.22923947X-RAY DIFFRACTION97
2.0581-2.08630.27072090.22173981X-RAY DIFFRACTION99
2.0863-2.11610.2932080.21493954X-RAY DIFFRACTION98
2.1161-2.14760.2692100.20963986X-RAY DIFFRACTION98
2.1476-2.18120.25582100.19863987X-RAY DIFFRACTION99
2.1812-2.2170.24342090.1943994X-RAY DIFFRACTION98
2.217-2.25520.25262100.19063981X-RAY DIFFRACTION99
2.2552-2.29620.23872100.19213974X-RAY DIFFRACTION98
2.2962-2.34040.21642090.18483962X-RAY DIFFRACTION98
2.3404-2.38820.22982020.18073861X-RAY DIFFRACTION94
2.3882-2.44010.24482100.17223980X-RAY DIFFRACTION99
2.4401-2.49690.2252110.17334019X-RAY DIFFRACTION98
2.4969-2.55930.24842110.17544001X-RAY DIFFRACTION98
2.5593-2.62850.21392130.1744035X-RAY DIFFRACTION99
2.6285-2.70590.21882110.1764025X-RAY DIFFRACTION99
2.7059-2.79320.21332130.17514048X-RAY DIFFRACTION99
2.7932-2.8930.23592130.17384037X-RAY DIFFRACTION99
2.893-3.00890.21252130.17234048X-RAY DIFFRACTION99
3.0089-3.14580.20782060.16563915X-RAY DIFFRACTION96
3.1458-3.31170.18362150.16224094X-RAY DIFFRACTION100
3.3117-3.51920.18742160.15094097X-RAY DIFFRACTION100
3.5192-3.79090.1562150.1394090X-RAY DIFFRACTION100
3.7909-4.17240.14452190.13474149X-RAY DIFFRACTION100
4.1724-4.77620.1562090.12793980X-RAY DIFFRACTION96
4.7762-6.01740.1832210.1524189X-RAY DIFFRACTION100
6.0174-98.27810.19562250.16754270X-RAY DIFFRACTION97

+
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