4P4L | pdb_00004p4l

Crystal Structure of Mycobacterium tuberculosis Shikimate Dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb4P4L/pdb

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


• Deposited: 2014-03-12 Released: 2015-03-18 
• Deposition Author(s): Lalgondar, M., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structure of Mycobacterium tuberculosis Shikimate Dehydrogenase

Lalgondar, M., Sacchettini, J.C.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.87 kDa 
• Atom Count: 5,759 
• Modeled Residue Count: 784 
• Deposited Residue Count: 831 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)	A, B, C	277	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: aroE, MT2629, Rv2552c EC: 1.1.1.25
UniProt
Find proteins for I6Y120 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y120  Go to UniProtKB:  I6Y120

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SKM	D [auth A], G [auth B], I [auth C]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C7 H10 O5 JXOHGGNKMLTUBP-HSUXUTPPSA-N
SO4	E [auth A], F [auth A], H [auth B], J [auth C], K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.703	α = 90
b = 132.315	β = 90
c = 38.465	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Lalgondar, M., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-03-27
  Changes: Refinement description