3SHP | pdb_00003shp

Crystal structure of putative acetyltransferase from Sphaerobacter thermophilus DSM 20745

PDB DOI: https://doi.org/10.2210/pdb3SHP/pdb

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

Deposited: 2011-06-16 Released: 2011-07-06
Deposition Author(s): Chang, C., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of putative acetyltransferase from Sphaerobacter thermophilus DSM 20745

Chang, C., Li, H., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 39.93 kDa
Atom Count: 2,884
Modeled Residue Count: 326
Deposited Residue Count: 352
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acetyltransferase Sthe_0691	A, B	176	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0 Gene Names: Sthe_0691
UniProt
Find proteins for D1C1L1 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C1L1 Go to UniProtKB: D1C1L1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1C1L1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRT Query on SRT Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.196	α = 90
b = 89.196	β = 90
c = 115.726	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-07-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-07-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, 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.