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), 0.291 (DCC)
R-Value Work:
0.263 (Depositor), 0.262 (DCC)
R-Value Observed:
0.291 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.291 (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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.