3L3S | pdb_00003l3s

Crystal structure of an enoyl-CoA hydrotase/isomerase family protein from Silicibacter pomeroyi

• PDB DOI: https://doi.org/10.2210/pdb3L3S/pdb

• Classification: ISOMERASE
• Organism(s): Ruegeria pomeroyi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-17 Released: 2010-01-05 
• Deposition Author(s): Eswaramoorthy, S., Silberstein, M., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.294 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.291 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an enoyl-CoA hydrotase/isomerase family protein from Silicibacter pomeroyi

Eswaramoorthy, S., Silberstein, M., Burley, S.K., 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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 342.74 kDa 
• Atom Count: 20,649 
• Modeled Residue Count: 2,789 
• Deposited Residue Count: 3,156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase family protein	A, B, C, D, E, F, G, H, I, J, K, L	263	Ruegeria pomeroyi	Mutation(s): 0  Gene Names: SPO2339
UniProt
Find proteins for Q5LQZ3 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LQZ3  Go to UniProtKB:  Q5LQZ3

Small Molecules

Non-standard Monomers  2 Unique
ID	Chains	Type	Formula	2D Diagram
MSE	A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C5 H11 N O2 Se
OCS	A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C3 H7 N O5 S

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.294 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.291 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.403	α = 90
b = 124.285	β = 102.44
c = 146.999	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-05 
Deposition Author(s): Eswaramoorthy, S., Silberstein, M., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection