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- PDB-6k6r: Crystal structure of Saccharomyces cerevisiae single domain sulfu... -

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Basic information

Entry
Database: PDB / ID: 6k6r
TitleCrystal structure of Saccharomyces cerevisiae single domain sulfurtranferase RDL2
ComponentsThiosulfate sulfurtransferase RDL2, mitochondrial
KeywordsTRANSFERASE / thiosulfate:cyanide sulfurtransferase / Rhodanese / Saccharomyces cerevisiae
Function / homology
Function and homology information


thiosulfate sulfurtransferase / sulfur compound metabolic process / thiosulfate-cyanide sulfurtransferase activity / mitochondrion
Similarity search - Function
Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiosulfate sulfurtransferase RDL2, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.471 Å
AuthorsLi, H.J. / Wang, Q.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China91751207, 31770093 China
CitationJournal: Antioxidants / Year: 2021
Title: Saccharomyces cerevisiaeRhodanese RDL2 Uses the ArgResidue of the Active-Site Loop for Thiosulfate Decomposition
Authors: Wang, Q.D. / Li, H. / Xia, Y. / Xun, L. / Li, H.J.
History
DepositionJun 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiosulfate sulfurtransferase RDL2, mitochondrial
D: Thiosulfate sulfurtransferase RDL2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)33,5172
Polymers33,5172
Non-polymers00
Water1,20767
1
A: Thiosulfate sulfurtransferase RDL2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Thiosulfate sulfurtransferase RDL2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.753, 79.753, 110.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11D-217-

HOH

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Components

#1: Protein Thiosulfate sulfurtransferase RDL2, mitochondrial / Altered inheritance of mitochondria protein 42 / Found in mitochondrial proteome protein 31 / ...Altered inheritance of mitochondria protein 42 / Found in mitochondrial proteome protein 31 / Rhodanese-like protein 2


Mass: 16758.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RDL2, AIM42, FMP31, YOR286W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q08742, thiosulfate sulfurtransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3.5M Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 11448 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.99 / Net I/σ(I): 24.69
Reflection shellResolution: 2.47→2.51 Å

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D1P

3d1p


Resolution: 2.471→27.595 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2472 --
Rwork0.2077 --
obs-11448 99.7 %
Refinement stepCycle: LAST / Resolution: 2.471→27.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 67 2019

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