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- PDB-3aax: Crystal structure of probable thiosulfate sulfurtransferase cysa3... -

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Basic information

Entry
Database: PDB / ID: 3aax
TitleCrystal structure of probable thiosulfate sulfurtransferase cysa3 (RV3117) from Mycobacterium tuberculosis: monoclinic FORM
ComponentsPutative thiosulfate sulfurtransferaseRhodanese
KeywordsTRANSFERASE / M. tuberculosis / sulfurtransferase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium (TBSGC)
Function / homology
Function and homology information


thiosulfate sulfurtransferase / thiosulfate 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 / 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: 2.5 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: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Putative thiosulfate sulfurtransferase
B: Putative thiosulfate sulfurtransferase


Theoretical massNumber of molelcules
Total (without water)62,1052
Polymers62,1052
Non-polymers00
Water1,22568
1
A: Putative thiosulfate sulfurtransferase


Theoretical massNumber of molelcules
Total (without water)31,0531
Polymers31,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative thiosulfate sulfurtransferase


Theoretical massNumber of molelcules
Total (without water)31,0531
Polymers31,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.862, 91.428, 83.569
Angle α, β, γ (deg.)90.00, 96.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31052.516 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein concentration 8mg/ml, 0.1M Tris HCl pH 8.5, Precipitant 0.2M MgCl2, 25% PEG 3350., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2007
RadiationMonochromator: Double flat crystal, Si(iii) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.5→45.7 Å / Num. all: 20078 / Num. obs: 20078 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2006 / % possible all: 98

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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: 2.5→41.51 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.888 / SU B: 13.117 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 1.091 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE ELECTRON DENSITY FOR THE RESIDUES 1-3,180-181 IN CHAIN A AND RESIDUE 177 IN CHAIN B, IS NOT RESOLVED. HENCE, THESE RESIDUES WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.29123 1028 5.2 %RANDOM
Rwork0.23393 ---
obs0.23696 18909 98.75 %-
all-18909 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.363 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å20.87 Å2
2--0.56 Å20 Å2
3----3.99 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4329 0 0 68 4397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224437
X-RAY DIFFRACTIONr_angle_refined_deg0.9021.9436034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2895544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74824.072221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04815703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6741531
X-RAY DIFFRACTIONr_chiral_restr0.0690.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213471
X-RAY DIFFRACTIONr_mcbond_it0.3271.52727
X-RAY DIFFRACTIONr_mcangle_it0.60824373
X-RAY DIFFRACTIONr_scbond_it0.63431710
X-RAY DIFFRACTIONr_scangle_it1.0974.51661
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 78 -
Rwork0.321 1392 -
obs--97.61 %

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