3US8 | pdb_00003us8

Crystal Structure of an isocitrate dehydrogenase from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb3US8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-23 Released: 2011-12-14 
• Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal Structure of an isocitrate dehydrogenase from Sinorhizobium meliloti 1021

Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.07 kDa 
• Atom Count: 6,705 
• Modeled Residue Count: 802 
• Deposited Residue Count: 854 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP]	A, B	427	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: icd, R01792, SMc00480 EC: 1.1.1.42
UniProt
Find proteins for Q92PG6 (Rhizobium meliloti (strain 1021)) Explore Q92PG6  Go to UniProtKB:  Q92PG6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.458	α = 90
b = 96.208	β = 90
c = 146.538	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary