9IJB

Crystal structure and function analysis of a highly potential drug target 6-phosphogluconate dehydrogenase in Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb9IJB/pdb

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


• Deposited: 2024-06-22 Released: 2024-07-03 
• Deposition Author(s): Wang, Y.Z., Ren, X.Q., Li, T., Zhang, R.D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.251 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

Crystal structure and function analysis of a potential drug target 6-phosphogluconate dehydrogenase in Mycobacterium tuberculosis

Wang, Y.Z., Ren, X.Q., Li, T., Zhang, R.D.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 145.6 kDa 
• Atom Count: 9,968 
• Modelled Residue Count: 1,310 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase, NAD(+)-dependent, decarboxylating	A, B, C, D	340	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  gnd2, gntZ, A4S10_01196, ERS007681_00218, ERS007718_03264, ERS007720_01707, ERS007741_00547, ERS027646_01529, ERS027661_00118, ERS035788_00611, ERS053720_03175, SAMEA2683035_02610 EC: 1.1.1.343 (PDB Primary Data), 1.1.1.44 (PDB Primary Data)
UniProt
Find proteins for A0A045IPA0 (Mycobacterium tuberculosis) Explore A0A045IPA0  Go to UniProtKB:  A0A045IPA0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.251 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.991	α = 90
b = 107.246	β = 90
c = 137.023	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Wang, Y.Z., Ren, X.Q., Li, T., Zhang, R.D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2017YFA0504300
National Natural Science Foundation of China (NSFC)	China	2017YFA0505900
National Natural Science Foundation of China (NSFC)	China	32360046

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release