3T7B | pdb_00003t7b

Crystal Structure of N-acetyl-L-glutamate kinase from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3T7B/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-29 Released: 2011-09-14 
• Deposition Author(s): Demas, M.W., Solberg, R.G., Cooper, D.R., Chruszcz, M., Porebski, P.J., Zheng, H., Onopriyenko, O., Skarina, T., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.213 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal Structure of N-acetyl-L-glutamate kinase from Yersinia pestis

Demas, M.W., Solberg, R.G., Cooper, D.R., Chruszcz, M., Porebski, P.J., Zheng, H., Onopriyenko, O., Skarina, T., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 55.41 kDa 
• Atom Count: 3,881 
• Modeled Residue Count: 513 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylglutamate kinase	A, B	260	Yersinia pestis CO92	Mutation(s): 0  Gene Names: argB, y0311, YPO3925, YP_3124 EC: 2.7.2.8
UniProt
Find proteins for Q8ZA87 (Yersinia pestis) Explore Q8ZA87  Go to UniProtKB:  Q8ZA87

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT	E [auth B]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
GLU	C [auth A], D [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N

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: 2.50 Å
• R-Value Free:  0.213 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33T7B

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.456	α = 90
b = 134.688	β = 90
c = 98.02	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-14 
Deposition Author(s): Demas, M.W., Solberg, R.G., Cooper, D.R., Chruszcz, M., Porebski, P.J., Zheng, H., Onopriyenko, O., Skarina, T., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-09-14
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Structure summary