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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.294 (Depositor), 0.280 (DCC)
R-Value Work:
0.263 (Depositor), 0.260 (DCC)
R-Value Observed:
0.291 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase family protein	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LQZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
OCS Query on OCS	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.294 (Depositor), 0.280 (DCC)
R-Value Work: 0.263 (Depositor), 0.260 (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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-01-05

Deposition Author(s):

Eswaramoorthy, S.

Silberstein, M.

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.