3PYD

crystal structure of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb3PYD/pdb

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


• Deposited: 2010-12-13 Released: 2012-01-25 
• Deposition Author(s): Shan, S., Chen, X.H., Liu, T., Zhao, H.C., Rao, Z.H., Lou, Z.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

The Structural Basis for anti-TB Drug Discovery targeting of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis

Shan, S., Chen, X.H., Liu, T., Zhao, H.C., Rao, Z.H., Lou, Z.Y.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 31.5 kDa 
• Atom Count: 2,349 
• Modelled Residue Count: 298 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	A	306	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: ispE, Rv1011, MT1040, MTCI237.28 EC: 2.7.1.148
UniProt
Find proteins for P9WKG7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKG7  Go to UniProtKB:  P9WKG7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.584	α = 90
b = 72.375	β = 90
c = 107.393	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Shan, S., Chen, X.H., Liu, T., Zhao, H.C., Rao, Z.H., Lou, Z.Y.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description