6K6R

Crystal structure of Saccharomyces cerevisiae single domain sulfurtranferase RDL2

PDB DOI: https://doi.org/10.2210/pdb6K6R/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-06-04 Released: 2019-11-06
Deposition Author(s): Li, H.J., Wang, Q.D.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.247
R-Value Work: 0.208

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Saccharomyces cerevisiaeRhodanese RDL2 Uses the ArgResidue of the Active-Site Loop for Thiosulfate Decomposition

Wang, Q.D., Li, H., Xia, Y., Xun, L., Li, H.J.

(2021) Antioxidants (Basel) 10

DOI: https://doi.org/doi.org/10.3390/antiox10101525

Macromolecule Content

Total Structure Weight: 33.52 kDa
Atom Count: 2,017
Modelled Residue Count: 246
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiosulfate sulfurtransferase RDL2, mitochondrial	A, B [auth D]	149	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RDL2, AIM42, FMP31, YOR286W EC: 2.8.1.1
UniProt
Find proteins for Q08742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08742 Go to UniProtKB: Q08742
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A, B [auth D]	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.247
R-Value Work: 0.208
Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.753	α = 90
b = 79.753	β = 90
c = 110.382	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91751207, 31770093

Revision History (Full details and data files)

Version 1.0: 2019-11-06
Type: Initial release
Version 1.1: 2021-10-06
Changes: Database references, Derived calculations
Version 1.2: 2023-11-22
Changes: Data collection, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary

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.