4K29 | pdb_00004k29

Crystal structure of an enoyl-CoA hydratase/isomerase from Xanthobacter autotrophicus Py2

• PDB DOI: https://doi.org/10.2210/pdb4K29/pdb

• Classification: ISOMERASE
• Organism(s): Xanthobacter versatilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-04-08 Released: 2013-04-24 
• Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, F., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.198 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of an enoyl-CoA hydratase/isomerase from Xanthobacter autotrophicus Py2

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.34 kDa 
• Atom Count: 6,703 
• Modeled Residue Count: 805 
• Deposited Residue Count: 885 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase	A, B, C	295	Xanthobacter versatilis	Mutation(s): 0  Gene Names: Xaut_3350
UniProt
Find proteins for A7IKN6 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)) Explore A7IKN6  Go to UniProtKB:  A7IKN6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	D [auth A], F [auth C], G [auth C]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL	E [auth A], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.198 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.052	α = 90
b = 144.576	β = 90
c = 129.568	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, F., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary