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- PDB-3aay: Crystal structure of probable thiosulfate sulfurtransferase CYSA3... -

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Basic information

Entry
Database: PDB / ID: 3aay
TitleCrystal structure of probable thiosulfate sulfurtransferase CYSA3 (RV3117) from Mycobacterium tuberculosis: orthorhombic form
ComponentsPutative thiosulfate sulfurtransferase
KeywordsTRANSFERASE / M. tuberculosis / sulfurtranserase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium (TBSGC)
Function / homology
Function and homology information


thiosulfate sulfurtransferase / thiosulfate-cyanide sulfurtransferase activity / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
: / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain ...: / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / 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
Putative thiosulfate sulfurtransferase / Putative thiosulfate sulfurtransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSankaranarayanan, R. / Witholt, S.J. / Cherney, M.M. / Garen, C.R. / Cherney, L.T. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: To be Published
Title: The crystal structure of probable thiosulfate sulfurtransferase CysA3 (Rv3117) from Mycobacterium tuberculosis
Authors: Sankaranarayanan, R. / Witholt, S.J. / Cherney, M.M. / Garen, C.R. / Cherney, L.T. / James, M.N.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Expression, purification, crystallization and preliminary X-ray analysis of Rv3117, a probable thiosulfate sulfurtransferase (CysA3) from Mycobacterium tuberculosis
Authors: Witholt, S.J. / Sankaranarayanan, R. / Garen, C.R. / Cherney, M.M. / Cherney, L.T. / James, M.N.G.
History
DepositionNov 28, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative thiosulfate sulfurtransferase
B: Putative thiosulfate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6988
Polymers62,1372
Non-polymers5616
Water8,251458
1
A: Putative thiosulfate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3494
Polymers31,0691
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative thiosulfate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3494
Polymers31,0691
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.431, 84.141, 102.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative thiosulfate sulfurtransferase / Rhodanese-like protein


Mass: 31068.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: CysA3 / Plasmid: pDEST-17 / Production host: Escherichia coli (E. coli)
References: UniProt: O05793, UniProt: P9WHF9*PLUS, thiosulfate sulfurtransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein Concentration 8 mg/ml in Tris Buffer pH 7.5, Precipitant 0.1M Bis-Tris at pH 5.5, 3% MPD, 5mM sodium thiosulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.976067 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2008
Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976067 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 47968 / Num. obs: 47968 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4717 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UAR

1uar


Resolution: 1.9→37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.259 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE ELECTRON DENSITY FOR THE RESIDUES 176-180 IN CHAIN A IS NOT RESOLVED. HENCE, THESE RESIDUES WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24187 1486 3.1 %RANDOM
Rwork0.18864 ---
all0.19027 46409 --
obs0.19027 46409 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---1.18 Å20 Å2
3---1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 34 458 4838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224489
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9526097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1624.081223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43515712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg181532
X-RAY DIFFRACTIONr_chiral_restr0.0910.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213482
X-RAY DIFFRACTIONr_mcbond_it0.6991.52736
X-RAY DIFFRACTIONr_mcangle_it1.324394
X-RAY DIFFRACTIONr_scbond_it2.02431753
X-RAY DIFFRACTIONr_scangle_it3.3224.51703
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 110 -
Rwork0.222 3349 -
obs--99.23 %

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