6N2O

2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus with 2-oxoglutarate, coenzyme A and succinyl-CoA bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.824 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A reverse TCA cycle 2-oxoacid:ferredoxin oxidoreductase that makes C-C bonds from CO2

Chen, P.Y.-T.Li, B.Drennan, C.L.Elliott, S.J.

(2019) Joule 3: 595-611


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein
A, C
573Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1)Mutation(s): 0 
Find proteins for A0L8G4 (Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1))
Go to UniProtKB:  A0L8G4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit
B, D
292Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1)Mutation(s): 0 
Find proteins for A0L8G5 (Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1))
Go to UniProtKB:  A0L8G5
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
B, D
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
SF4
Query on SF4

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Download CCD File 
B, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
SCA
Query on SCA

Download SDF File 
Download CCD File 
C
SUCCINYL-COENZYME A
C25 H40 N7 O19 P3 S
VNOYUJKHFWYWIR-ITIYDSSPSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.824 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.407α = 90.00
b = 100.532β = 90.00
c = 202.053γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35-GM126982

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release