3JU1 | pdb_00003ju1

Crystal Structure of Enoyl-CoA Hydratase/Isomerase Family Protein

• PDB DOI: https://doi.org/10.2210/pdb3JU1/pdb

• Classification: lyase, isomerase
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-09-14 Released: 2009-09-22 
• Deposition Author(s): Kim, Y., Xu, X., Cui, H., Ng, J., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.231 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal Structure of Enoyl-CoA Hydratase/Isomerase Family Protein

Kim, Y., Xu, X., Cui, H., Ng, J., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.98 kDa 
• Atom Count: 6,056 
• Modeled Residue Count: 721 
• Deposited Residue Count: 814 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase family protein	A, B	407	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: SO_1681 EC: 3.1.2.4
UniProt
Find proteins for Q8EGC3 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EGC3  Go to UniProtKB:  Q8EGC3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	C [auth A], H [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
FMT	D [auth A], E [auth A], G [auth B], I [auth B], J [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.231 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.982	α = 90
b = 83.982	β = 90
c = 277.832	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Kim, Y., Xu, X., Cui, H., Ng, J., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary