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- PDB-8agf: Crystal structure of human Thiosulfate sulfurtransferase amino ac... -

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Basic information

Entry
Database: PDB / ID: 8agf
TitleCrystal structure of human Thiosulfate sulfurtransferase amino acids 2-297
ComponentsThiosulfate sulfurtransferaseRhodanese
KeywordsSTRUCTURAL PROTEIN / MITOCANDRIAL ENZYME Human chromosome 22
Function / homology
Function and homology information


sulfur amino acid catabolic process / rRNA transport / cyanate catabolic process / Sulfide oxidation to sulfate / thiosulfate sulfurtransferase / Degradation of cysteine and homocysteine / thiosulfate sulfurtransferase activity / rRNA import into mitochondrion / transsulfuration / epithelial cell differentiation ...sulfur amino acid catabolic process / rRNA transport / cyanate catabolic process / Sulfide oxidation to sulfate / thiosulfate sulfurtransferase / Degradation of cysteine and homocysteine / thiosulfate sulfurtransferase activity / rRNA import into mitochondrion / transsulfuration / epithelial cell differentiation / 5S rRNA binding / mitochondrial matrix / mitochondrion / extracellular space
Similarity search - Function
Sulfurtransferase TST/MPST-like / Rhodanese signature 1. / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain
Similarity search - Domain/homology
Thiosulfate sulfurtransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsGoor, H.v. / Grove, M.R. / AL-Dahmani, Z.m.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Dutch Kidney Foundation Netherlands
CitationJournal: To Be Published
Title: The crystal structure of human Thiosulfate sulfurtransferase
Authors: ALDahmani, Z. / Groves, M. / Goor, H. / Wang, C.
History
DepositionJul 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiosulfate sulfurtransferase


Theoretical massNumber of molelcules
Total (without water)32,6491
Polymers32,6491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.930, 48.543, 152.501
Angle α, β, γ (deg.)90.000, 96.369, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Thiosulfate sulfurtransferase / Rhodanese / Rhodanese


Mass: 32648.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TST / Production host: Escherichia coli (E. coli) / References: UniProt: Q16762, thiosulfate sulfurtransferase

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000, Tris, calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.4→46.272 Å / Num. obs: 4269 / % possible obs: 98.9 % / Redundancy: 6.8 % / CC1/2: 0.878 / Rmerge(I) obs: 0.599 / Rpim(I) all: 0.368 / Rrim(I) all: 0.705 / Net I/σ(I): 6.2
Reflection shellResolution: 9→46.23 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.118 / Num. unique obs: 4269 / CC1/2: 0.992 / Rpim(I) all: 0.071 / Rrim(I) all: 0.138

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOH

1boh


Resolution: 3.4→46.272 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.801 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.171 / SU B: 89.159 / SU ML: 0.619 / Average fsc free: 0.856 / Average fsc work: 0.902 / Cross valid method: FREE R-VALUE / ESU R Free: 0.73
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2781 226 5.296 %
Rwork0.1956 4041 -
all0.2 --
obs-4267 98.522 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.817 Å2
Baniso -1Baniso -2Baniso -3
1--2.789 Å20 Å2-0.006 Å2
2--2.08 Å2-0 Å2
3---0.693 Å2
Refinement stepCycle: LAST / Resolution: 3.4→46.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 0 0 2302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132366
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152188
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.6483207
X-RAY DIFFRACTIONr_angle_other_deg1.161.5775041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2325289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49220.149134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.82215383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6471523
X-RAY DIFFRACTIONr_chiral_restr0.0580.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022673
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02581
X-RAY DIFFRACTIONr_nbd_refined0.2410.2658
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22410
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21117
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0560.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2870.218
X-RAY DIFFRACTIONr_nbd_other0.2850.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0570.22
X-RAY DIFFRACTIONr_mcbond_it0.3761.6831159
X-RAY DIFFRACTIONr_mcbond_other0.3661.6821158
X-RAY DIFFRACTIONr_mcangle_it0.6762.5231447
X-RAY DIFFRACTIONr_mcangle_other0.6772.5251448
X-RAY DIFFRACTIONr_scbond_it0.2991.7211206
X-RAY DIFFRACTIONr_scbond_other0.2991.7211206
X-RAY DIFFRACTIONr_scangle_it0.5572.5611760
X-RAY DIFFRACTIONr_scangle_other0.5572.5621761
X-RAY DIFFRACTIONr_lrange_it1.43919.6932789
X-RAY DIFFRACTIONr_lrange_other1.43819.7012790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.4880.354170.246286X-RAY DIFFRACTION92.6606
3.488-3.5840.416200.243269X-RAY DIFFRACTION98.9726
3.584-3.6870.359150.214291X-RAY DIFFRACTION100
3.687-3.8010.267120.216283X-RAY DIFFRACTION100
3.801-3.9250.255130.204251X-RAY DIFFRACTION100
3.925-4.0620.34780.18284X-RAY DIFFRACTION100
4.062-4.2150.196130.178252X-RAY DIFFRACTION99.6241
4.387-4.5810.215140.167234X-RAY DIFFRACTION98.4127
4.581-4.8040.237150.16213X-RAY DIFFRACTION99.1304
4.804-5.0630.22680.194211X-RAY DIFFRACTION100
5.063-5.3680.36180.205215X-RAY DIFFRACTION98.6726
5.368-5.7370.257110.212171X-RAY DIFFRACTION98.913
5.737-6.1930.2980.2178X-RAY DIFFRACTION97.3822
6.193-6.780.334150.205144X-RAY DIFFRACTION94.6429
6.78-7.5730.227140.173139X-RAY DIFFRACTION96.8354
7.573-8.730.393110.154129X-RAY DIFFRACTION100
8.73-10.6560.0920.152125X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.7928 Å / Origin y: -24.5208 Å / Origin z: -22.4109 Å
111213212223313233
T0.1304 Å2-0.0213 Å20.0488 Å2-0.0333 Å2-0.0111 Å2--0.0274 Å2
L0.9961 °2-0.1472 °20.4814 °2-1.3628 °2-0.4599 °2--1.0651 °2
S0.035 Å °0.0615 Å °-0.0072 Å °0.0026 Å °0.0034 Å °0.1101 Å °0.0034 Å °0.0416 Å °-0.0384 Å °
Refinement TLS groupSelection: ALL

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