3DR3 | pdb_00003dr3

Structure of IDP00107, a potential N-acetyl-gamma-glutamylphosphate reductase from Shigella flexneri

• PDB DOI: https://doi.org/10.2210/pdb3DR3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-10 Released: 2008-08-05 
• Deposition Author(s): Singer, A.U., Skarina, T., Onopriyenko, O., Edwards, A.M., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Structure of IDP00107, a potential N-acetyl-gamma-glutamylphosphate reductase from Shigella flexneri

Singer, A.U., Skarina, T., Onopriyenko, O., Edwards, A.M., Anderson, W.F., Savchenko, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.42 kDa 
• Atom Count: 2,963 
• Modeled Residue Count: 335 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyl-gamma-glutamyl-phosphate reductase	A	337	Shigella flexneri	Mutation(s): 0  Gene Names: argC, SF4035, S3711 EC: 1.2.1.38
UniProt
Find proteins for P59310 (Shigella flexneri) Explore P59310  Go to UniProtKB:  P59310

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLT	D [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33dr3

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.299	α = 90
b = 117.299	β = 90
c = 115.472	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Singer, A.U., Skarina, T., Onopriyenko, O., Edwards, A.M., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description