3S1T | pdb_00003s1t

Structure of the regulatory domain of aspartokinase (Rv3709c; AK-beta) in complex with threonine from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb3S1T/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-16 Released: 2012-06-13 
• Deposition Author(s): Schuldt, L., Mueller-Dieckmann, J., Weiss, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

High-resolution X-ray structure of the regulatory domain of the mycobacterial aspartokinase in complex with threonine

Schuldt, L., Mueller-Dieckmann, J., Weiss, M.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Macromolecule Content 

• Total Structure Weight: 40.78 kDa 
• Atom Count: 2,713 
• Modeled Residue Count: 325 
• Deposited Residue Count: 373 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartokinase	A, B	181	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ask, MT3812, MTV025.057c, Rv3709c EC: 2.7.2.4
UniProt
Find proteins for P9WPX3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX3  Go to UniProtKB:  P9WPX3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartokinase	C	11	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  EC: 2.7.2.4
UniProt
Find proteins for P9WPX3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX3  Go to UniProtKB:  P9WPX3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THR	D [auth A], I [auth B]	THREONINE C4 H9 N O3 AYFVYJQAPQTCCC-GBXIJSLDSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.7	α = 90
b = 63.43	β = 90
c = 108.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Schuldt, L., Mueller-Dieckmann, J., Weiss, M.S.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description