8X5S | pdb_00008x5s

Crystal structure of shikimate kinase of Mycobacterium tuberculosis complex with shikimate-3-phosphate

• PDB DOI: https://doi.org/10.2210/pdb8X5S/pdb

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


• Deposited: 2023-11-18 Released: 2024-11-20 
• Deposition Author(s): Yadav, A.K., Madhuri, M., Saini, C., Inampudi, K.K., Ethayathulla, A.S., Kumar, M.
• Funding Organization(s): Indian Council of Medical Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.188 (DCC) 

Starting Model: experimental

Literature

Crystal structure of shikimate kinase of Mycobacterium tuberculosis complex with shikimate-3-phosphate

Yadav, A.K., Kumar, M., Ethayathulla, A.S., Madhuri, M., Saini, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.25 kDa 
• Atom Count: 1,476 
• Modeled Residue Count: 168 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate kinase	A	176	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: aroK EC: 2.7.1.71
UniProt
Find proteins for P9WPY3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPY3  Go to UniProtKB:  P9WPY3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S3P (Subject of Investigation/LOI)	B [auth A]	SHIKIMATE-3-PHOSPHATE C7 H11 O8 P QYOJSKGCWNAKGW-PBXRRBTRSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.188 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.424	α = 90
b = 59.424	β = 90
c = 102.25	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Yadav, A.K., Madhuri, M., Saini, C., Inampudi, K.K., Ethayathulla, A.S., Kumar, M.

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Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	--

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release