2AP9 | pdb_00002ap9

Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551

• PDB DOI: https://doi.org/10.2210/pdb2AP9/pdb

• Classification: SIGNALING PROTEIN,TRANSFERASE
• Organism(s): Mycobacterium tuberculosis CDC1551
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-08-15 Released: 2005-08-30 
• Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.284 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.267 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551

Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 191.89 kDa 
• Atom Count: 13,141 
• Modeled Residue Count: 1,762 
• Deposited Residue Count: 1,794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
acetylglutamate kinase	A, B, C, D, E, F	299	Mycobacterium tuberculosis CDC1551	Mutation(s): 7  Gene Names: argB, Rv1654, MT1692 EC: 2.7.2.8
UniProt
Find proteins for P9WQ01 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQ01  Go to UniProtKB:  P9WQ01

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	H [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
MG	G [auth A], I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.284 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.267 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.024	α = 90
b = 122.996	β = 90
c = 194.581	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-30 
Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-08-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary