3SEF

2.4 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate and NADPH

• PDB DOI: https://doi.org/10.2210/pdb3SEF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-10 Released: 2011-07-27 
• Deposition Author(s): Halavaty, A.S., Light, S.H., Minasov, G., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.276 
• R-Value Work: 0.235 
• R-Value Observed: 0.237 

Starting Model: experimental

Literature

2.4 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate and NADPH

Halavaty, A.S., Light, S.H., Minasov, G., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 133.94 kDa 
• Atom Count: 8,384 
• Modelled Residue Count: 1,053 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate 5-dehydrogenase	A, B, C, D	302	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: aroE, VC_0056 EC: 1.1.1.25
UniProt
Find proteins for Q9KVT3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVT3  Go to UniProtKB:  Q9KVT3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
SKM	G [auth B], H [auth C]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C7 H10 O5 JXOHGGNKMLTUBP-HSUXUTPPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.276 
• R-Value Work: 0.235 
• R-Value Observed: 0.237 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m33sef

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.03	α = 90
b = 86.079	β = 92.85
c = 81.018	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Halavaty, A.S., Light, S.H., Minasov, G., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2011-08-10
  Changes: Data collection
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description