4GFS

1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Nickel Bound at Active Site

• PDB DOI: https://doi.org/10.2210/pdb4GFS/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-08-03 Released: 2012-08-15 
• Deposition Author(s): Light, S.H., Minasov, G., Krishna, S.N., Shuvalova, L., Kwon, K., Lavie, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Nickel Bound at Active Site

Light, S.H., Minasov, G., Krishna, S.N., Shuvalova, L., Kwon, K., Lavie, A., Anderson, W.F.

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)

Macromolecule Content

• Total Structure Weight: 55.73 kDa 
• Atom Count: 4,084 
• Modelled Residue Count: 500 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B	255	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: aroD, STM1358 EC: 4.2.1.10
UniProt
Find proteins for P58687 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P58687  Go to UniProtKB:  P58687

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	I [auth B]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
NI	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m34gfs

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.679	α = 90
b = 74.468	β = 100.17
c = 63.566	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Light, S.H., Minasov, G., Krishna, S.N., Shuvalova, L., Kwon, K., Lavie, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description