3FS5 | pdb_00003fs5

Crystal structure of Saccharomyces cerevisiae Ygr203w, a homolog of single-domain rhodanese and Cdc25 phosphatase catalytic domain

PDB DOI: https://doi.org/10.2210/pdb3FS5/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-09 Released: 2009-06-23
Deposition Author(s): Yeo, H.K., Lee, J.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.205 (Depositor), 0.194 (DCC)
R-Value Work:
0.182 (Depositor), 0.196 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 3FS5

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

Literature

Crystal structure of Saccharomyces cerevisiae Ygr203w, a homolog of single-domain rhodanese and Cdc25 phosphatase catalytic domain

Yeo, H.K., Lee, J.Y.

(2009) Proteins 76: 520-524

PubMed: 19382206 Search on PubMed
DOI: https://doi.org/10.1002/prot.22420
Primary Citation Related Structures:
3FS5

Organizational Affiliation

Department of Life Science, Dongguk University, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 17.63 kDa
Atom Count: 1,323
Modeled Residue Count: 152
Deposited Residue Count: 152
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YGR203W	A	152	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: YGR203W EC: 3.1.3
UniProt
Find proteins for P42937 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P42937 Go to UniProtKB: P42937
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42937
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.205 (Depositor), 0.194 (DCC)
R-Value Work: 0.182 (Depositor), 0.196 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.482	α = 90
b = 50.954	β = 90
c = 91.952	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-06
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.