3LB0 | pdb_00003lb0

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Citrate Bound to the Active Site.

• PDB DOI: https://doi.org/10.2210/pdb3LB0/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-07 Released: 2010-01-26 
• Deposition Author(s): Minasov, G., Light, S.H., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.201 (Depositor) 
• R-Value Work: 
  0.160 (Depositor) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Citrate Bound to the Active Site.

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)

Macromolecule Content 

• Total Structure Weight: 60.56 kDa 
• Atom Count: 4,957 
• Modeled Residue Count: 510 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B	276	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
TRS	E [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.201 (Depositor) 
• R-Value Work:  0.160 (Depositor) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33lb0

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.888	α = 93.95
b = 45.853	β = 101.19
c = 80.816	γ = 105.49

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: 2010-01-26 
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: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description