3OKF

2.5 Angstrom Resolution Crystal Structure of 3-Dehydroquinate Synthase (aroB) from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb3OKF/pdb

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


• Deposited: 2010-08-24 Released: 2010-09-08 
• Deposition Author(s): Minasov, G., Light, S.H., 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: 2.50 Å
• R-Value Free: 0.223 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

2.5 Angstrom Resolution Crystal Structure of 3-Dehydroquinate Synthase (aroB) from Vibrio cholerae.

Minasov, G., Light, S.H., 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 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.83 kDa 
• Atom Count: 5,710 
• Modelled Residue Count: 712 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate synthase	A, B	390	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: aroB EC: 4.2.3.4
UniProt
Find proteins for Q9KNV2 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KNV2  Go to UniProtKB:  Q9KNV2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], L [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PO4	D [auth A], E [auth A], F [auth A], M [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.223 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/m33okf

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.14	α = 90
b = 80.14	β = 90
c = 262.965	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: 2010-09-08 
Deposition Author(s): Minasov, G., Light, S.H., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description