4U4E | pdb_00004u4e

Crystal structure of putative thiolase from Sphaerobacter thermophilus DSM 20745

PDB DOI: https://doi.org/10.2210/pdb4U4E/pdb

Classification: TRANSFERASE
Organism(s): Sphaerobacter thermophilus DSM 20745
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-23 Released: 2014-08-06
Deposition Author(s): Chang, C., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.221 (Depositor), 0.226 (DCC)
R-Value Work:
0.172 (Depositor), 0.179 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of putative thiolase from Sphaerobacter thermophilus DSM 20745

Chang, C., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 40.83 kDa
Atom Count: 2,701
Modeled Residue Count: 360
Deposited Residue Count: 383
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiolase	A	383	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0 Gene Names: Sthe_0538
UniProt
Find proteins for D1C159 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C159 Go to UniProtKB: D1C159
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1C159
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.221 (Depositor), 0.226 (DCC)
R-Value Work: 0.172 (Depositor), 0.179 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.54	α = 90
b = 75.54	β = 90
c = 123.494	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	phasing
Coot	model building
SBC-Collect	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary

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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.