6K6R | pdb_00006k6r

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 (Depositor), 0.248 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 246
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.248 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)

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

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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

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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.