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- PDB-6bev: Human Single Domain Sulfurtranferase TSTD1 -

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Basic information

Entry
Database: PDB / ID: 6bev
TitleHuman Single Domain Sulfurtranferase TSTD1
ComponentsThiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1
KeywordsTRANSFERASE / Sulfurtransferase
Function / homology
Function and homology information


thiosulfate-thiol sulfurtransferase activity / sulfide oxidation, using sulfide:quinone oxidoreductase / Sulfide oxidation to sulfate / Transferases; Transferring sulfur-containing groups; Sulfurtransferases / cytoplasmic ribonucleoprotein granule / perinuclear region of cytoplasm / cytosol / cytoplasm
Similarity search - Function
Thiosulfate:glutathione sulfurtransferase, mammal / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain
Similarity search - Domain/homology
Thiosulfate:glutathione sulfurtransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.043 Å
AuthorsMotl, N. / Akey, D.L. / Smith, J.L. / Banerjee, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112455 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008353 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Thiosulfate sulfurtransferase-like domain-containing 1 protein interacts with thioredoxin.
Authors: Libiad, M. / Motl, N. / Akey, D.L. / Sakamoto, N. / Fearon, E.R. / Smith, J.L. / Banerjee, R.
History
DepositionOct 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1
B: Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)29,4312
Polymers29,4312
Non-polymers00
Water8,161453
1
A: Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)14,7161
Polymers14,7161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)14,7161
Polymers14,7161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.903, 40.246, 47.201
Angle α, β, γ (deg.)113.310, 90.200, 117.500
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1


Mass: 14715.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSTD1, KAT / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8NFU3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.09 M sodium cacodylate, pH 6.5, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.04→23.403 Å / Num. obs: 101056 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 6.965 % / Biso Wilson estimate: 11.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.033 / Χ2: 1.046 / Net I/σ(I): 24.19 / Num. measured all: 703860
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.04-1.116.5940.5672.1910319817091156510.9530.61691.6
1.11-1.187.2820.2885.2711094916107152370.9830.3194.6
1.18-1.286.9020.1838.419824214913142340.9880.19895.4
1.28-1.47.0750.12312.619345913746132090.9940.13396.1
1.4-1.567.1610.07919.938601212426120110.9970.08696.7
1.56-1.816.5120.0530.536944710943106650.9980.05497.5
1.81-2.217.0560.02854.23640579262907910.03198
2.21-3.127.250.0280.16511427160705410.02298.5
3.12-23.4036.9850.016107.55273543959391610.01798.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
SOLVEphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.043→23.403 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 16.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1441 3935 1.99 %
Rwork0.1301 193972 -
obs0.1304 100881 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.69 Å2 / Biso mean: 18.8192 Å2 / Biso min: 3.89 Å2
Refinement stepCycle: final / Resolution: 1.043→23.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 0 547 2286
Biso mean---33.73 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062003
X-RAY DIFFRACTIONf_angle_d0.9812739
X-RAY DIFFRACTIONf_chiral_restr0.074286
X-RAY DIFFRACTIONf_plane_restr0.007382
X-RAY DIFFRACTIONf_dihedral_angle_d20.169773
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0432-1.05590.41891310.42686237636884
1.0559-1.06920.34731290.34916377650687
1.0692-1.08330.31411340.28766651678589
1.0833-1.09820.25651380.24986774691291
1.0982-1.11380.20571430.22486691683492
1.1138-1.13050.21041350.2056874700993
1.1305-1.14810.21641310.19966907703893
1.1481-1.1670.20341500.20126800695093
1.167-1.18710.20551290.18057024715394
1.1871-1.20870.23021390.16736797693693
1.2087-1.23190.16831490.15766901705094
1.2319-1.25710.14091440.1437015715994
1.2571-1.28440.13161460.1396911705794
1.2844-1.31430.16321290.1357060718994
1.3143-1.34710.15891450.13076997714295
1.3471-1.38350.16081400.12366939707995
1.3835-1.42430.16511440.12586993713795
1.4243-1.47020.11851480.11547004715295
1.4702-1.52280.15271510.11067088723995
1.5228-1.58370.13621310.10826923705495
1.5837-1.65580.11751440.11037067721196
1.6558-1.7430.11621350.10857108724396
1.743-1.85220.1291480.11817039718796
1.8522-1.99510.11421440.12157121726596
1.9951-2.19580.12241440.10997142728697
2.1958-2.51320.14851510.11527223737497
2.5132-3.16510.12331460.12357225737198
3.1651-23.4090.14981370.12787084722196

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