4XIJ | pdb_00004xij

Crystal Structure of a Shikimate 5-dehydrogenase from Mycobacterium fortuitum Determined by Iodide SAD Phasing

• PDB DOI: https://doi.org/10.2210/pdb4XIJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 = JCM 6387
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-07 Released: 2015-02-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Crystal Structure of a Shikimate 5-dehydrogenase from Mycobacterium fortuitum Determined by Iodide SAD Phasing

SSGCID, Dranow, D.M., Abendroth, J., Fairman, J.W., Lorimer, D., Edwards, T.E.

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: 28.96 kDa 
• Atom Count: 2,474 
• Modeled Residue Count: 268 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate 5-dehydrogenase	A	275	Mycolicibacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 = JCM 6387	Mutation(s): 0  Gene Names: aroE, MFORT_30634 EC: 1.1.1.25
UniProt
Find proteins for K0V1M6 (Mycolicibacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 = JCM 6387) Explore K0V1M6  Go to UniProtKB:  K0V1M6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34XIJ

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.86	α = 90
b = 93.86	β = 90
c = 53.08	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references