1YEY | pdb_00001yey

Crystal Structure of L-fuconate Dehydratase from Xanthomonas campestris pv. campestris str. ATCC 33913

• PDB DOI: https://doi.org/10.2210/pdb1YEY/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Xanthomonas campestris pv. campestris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-28 Released: 2005-01-11 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Yew, W.S., Gerlt, J.A., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.272 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Literature

Crystal Structure of L-fuconate Dehydratase from Xanthomonas campestris pv. campestris str. ATCC 33913

Fedorov, A.A., Fedorov, E.V., Yew, W.S., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 generated by PISA,PQS (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 195.63 kDa 
• Atom Count: 13,524 
• Modeled Residue Count: 1,725 
• Deposited Residue Count: 1,776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-fuconate dehydratase	A, B, C, D	444	Xanthomonas campestris pv. campestris	Mutation(s): 9  EC: 4.2.1.68
UniProt
Find proteins for Q8P3K2 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P3K2  Go to UniProtKB:  Q8P3K2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.272 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.527	α = 90
b = 130.527	β = 90
c = 193.749	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-11 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Yew, W.S., Gerlt, J.A., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-01-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Structure summary