4JOT | pdb_00004jot

Crystal structure of enoyl-CoA hydrotase from Deinococcus radiodurans R1

• PDB DOI: https://doi.org/10.2210/pdb4JOT/pdb

• Classification: LYASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-03-18 Released: 2013-04-17 
• 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: 1.94 Å
• R-Value Free: 
  0.220 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of enoyl-CoA hydrotase from Deinococcus radiodurans R1

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

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 29.9 kDa 
• Atom Count: 1,951 
• Modeled Residue Count: 255 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase, putative	A	279	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_0114
UniProt
Find proteins for Q9RY37 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RY37  Go to UniProtKB:  Q9RY37

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.220 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.892	α = 90
b = 117.892	β = 90
c = 117.892	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: 2013-04-17 
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: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary