7BR9 | pdb_00007br9

Crystal structure of mus musculus IRG1

• PDB DOI: https://doi.org/10.2210/pdb7BR9/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-27 Released: 2021-02-03 
• Deposition Author(s): Park, H.H., Chun, H.L.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of mouse IRG1 suggests that cis-aconitate decarboxylase has an open and closed conformation.

Chun, H.L., Lee, S.Y., Kim, K.H., Lee, C.S., Oh, T.J., Park, H.H.

(2020) PLoS One 15: e0242383-e0242383

• PubMed: 33259501 
• DOI: https://doi.org/10.1371/journal.pone.0242383
• Primary Citation of Related Structures:  
  7BR9


• PubMed Abstract: 
  

  Coordinate and structural factors were deposited with the Protein Data Bank under PDB ID: 7BR9.

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Organizational Affiliation: 
• College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea.
Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea.
College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, Republic of Korea.
Genome-based BioIT Convergence Institute, Asan, Republic of Korea.
Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Republic of Korea.

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)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 107.63 kDa 
• Atom Count: 6,986 
• Modeled Residue Count: 900 
• Deposited Residue Count: 976 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cis-aconitate decarboxylase	A, B	488	Mus musculus	Mutation(s): 0  Gene Names: Acod1, Irg1 EC: 4.1.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P54987 (Mus musculus) Explore P54987  Go to UniProtKB:  P54987
IMPC:  MGI:103206

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.493	α = 90
b = 55.61	β = 107.67
c = 90.956	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Park, H.H., Chun, H.L.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description