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- PDB-8q5z: Crystal structure of bovine Thiosulfate sulfurtransferase -

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Basic information

Entry
Database: PDB / ID: 8q5z
TitleCrystal structure of bovine Thiosulfate sulfurtransferase
ComponentsThiosulfate sulfurtransferase
KeywordsSTRUCTURAL PROTEIN / mitochondrial enzyme
Function / homology
Function and homology information


rRNA transport / 3-mercaptopyruvate sulfurtransferase activity / thiosulfate sulfurtransferase / thiosulfate sulfurtransferase activity / rRNA import into mitochondrion / 5S rRNA binding / mitochondrial matrix / mitochondrion
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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGoor, H.v. / Groves, M.R. / AL-Dahmani, Z.M. / Wang, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Dutch Kidney Foundation Netherlands
CitationJournal: To Be Published
Title: Crystal structure of bovine Thiosulfate sulfurtransferase
Authors: AL-Dahmani, Z.M. / Groves, M.R. / Goo, H.v.
History
DepositionAug 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
SupersessionFeb 14, 2024ID: 8BGQ
Revision 1.1Feb 14, 2024Group: Advisory / Category: pdbx_database_PDB_obs_spr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiosulfate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3632
Polymers33,3401
Non-polymers231
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.857, 49.506, 41.863
Angle α, β, γ (deg.)90.000, 98.504, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thiosulfate sulfurtransferase


Mass: 33339.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: TST / Production host: Escherichia coli (E. coli) / References: UniProt: P00586
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, Tris, calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03322 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.5→38.86 Å / Num. obs: 47923 / % possible obs: 96.2 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.9
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.176 / Num. unique obs: 1966 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→38.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.786 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1628 2367 4.939 %
Rwork0.1463 45554 -
all0.147 --
obs-47921 95.834 %
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: 12.056 Å2
Baniso -1Baniso -2Baniso -3
1--0.253 Å20 Å20.155 Å2
2--0.066 Å2-0 Å2
3---0.134 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 1 293 2611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152223
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.6453290
X-RAY DIFFRACTIONr_angle_other_deg1.5691.5775127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.56720.827133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.3415387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.061520
X-RAY DIFFRACTIONr_chiral_restr0.10.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022763
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02589
X-RAY DIFFRACTIONr_nbd_refined0.2380.2477
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.22069
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21186
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2168
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.370.212
X-RAY DIFFRACTIONr_nbd_other0.3140.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.219
X-RAY DIFFRACTIONr_mcbond_it1.1241.0371183
X-RAY DIFFRACTIONr_mcbond_other1.121.0351182
X-RAY DIFFRACTIONr_mcangle_it1.6691.5581484
X-RAY DIFFRACTIONr_mcangle_other1.6711.5591485
X-RAY DIFFRACTIONr_scbond_it2.3051.2921235
X-RAY DIFFRACTIONr_scbond_other2.2961.2921235
X-RAY DIFFRACTIONr_scangle_it3.4791.841806
X-RAY DIFFRACTIONr_scangle_other3.4761.841806
X-RAY DIFFRACTIONr_lrange_it4.32313.1072807
X-RAY DIFFRACTIONr_lrange_other4.2612.6752752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.1851540.1612930X-RAY DIFFRACTION85.0993
1.539-1.5810.1651730.1433270X-RAY DIFFRACTION95.4268
1.581-1.6270.1681610.1323193X-RAY DIFFRACTION96.5458
1.627-1.6770.1671450.1253178X-RAY DIFFRACTION97.1922
1.677-1.7320.1471580.1233017X-RAY DIFFRACTION98.1756
1.732-1.7930.1611630.1332969X-RAY DIFFRACTION97.6918
1.793-1.860.1691270.1472854X-RAY DIFFRACTION97.482
1.86-1.9360.1631490.1412689X-RAY DIFFRACTION96.5635
1.936-2.0220.1431500.1412656X-RAY DIFFRACTION98.2493
2.022-2.1210.161290.1372528X-RAY DIFFRACTION98.1892
2.121-2.2360.1551320.142423X-RAY DIFFRACTION98.3449
2.236-2.3710.1691020.1442300X-RAY DIFFRACTION98.2413
2.371-2.5350.1721080.1472133X-RAY DIFFRACTION97.9458
2.535-2.7370.174880.1531914X-RAY DIFFRACTION92.7711
2.737-2.9980.193820.1491817X-RAY DIFFRACTION95.7157
2.998-3.3520.1651060.1581613X-RAY DIFFRACTION95.7127
3.352-3.8690.159830.1521403X-RAY DIFFRACTION93.1661
3.869-4.7350.153700.1491203X-RAY DIFFRACTION94.5063
4.735-6.6840.179520.161915X-RAY DIFFRACTION91.572

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