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- PDB-3hwi: Crystal structure of probable thiosulfate sulfurtransferase Cysa2... -

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Basic information

Entry
Database: PDB / ID: 3hwi
TitleCrystal structure of probable thiosulfate sulfurtransferase Cysa2 (Rhodanese-like protein) from Mycobacterium tuberculosis
ComponentsThiosulfate sulfurtransferaseRhodanese
KeywordsTRANSFERASE / NIAID / SSGCID / Seattle Structural Center for Infectious Disease / deCODE / UW / SBRI / tuberculosis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJun 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiosulfate sulfurtransferase
B: Thiosulfate sulfurtransferase


Theoretical massNumber of molelcules
Total (without water)66,6842
Polymers66,6842
Non-polymers00
Water7,170398
1
A: Thiosulfate sulfurtransferase


Theoretical massNumber of molelcules
Total (without water)33,3421
Polymers33,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiosulfate sulfurtransferase


Theoretical massNumber of molelcules
Total (without water)33,3421
Polymers33,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.446, 69.622, 83.110
Angle α, β, γ (deg.)90.000, 108.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thiosulfate sulfurtransferase / Rhodanese / Rhodanese-like protein / Thiosulfate sulfurtransferase Cysa2


Mass: 33342.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv
Gene: cysA1, cysA, Rv3117, MT3199, MTCY164.27, cysA2, Rv0815c, MT0837, MTV043.07c
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.: 398 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ sparse matrix screen condition h10, 25% PEG 3350, 0.1 M BisTris pH 5.5, 0.2 M ammonium acetate, 37.4 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→30 Å / Num. obs: 24551 / % possible obs: 92.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.106 / Χ2: 1.026 / Net I/σ(I): 17.208
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 7.9 / Num. unique all: 2649 / Χ2: 1.032 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å31.86 Å
Translation1.98 Å31.86 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UAR

1uar


Resolution: 2.29→28.88 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU B: 6.461 / SU ML: 0.158 / SU R Cruickshank DPI: 0.419 / SU Rfree: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.42 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1231 5 %RANDOM
Rwork0.177 ---
obs0.18 24466 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.9 Å2 / Biso mean: 22.807 Å2 / Biso min: 4.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å2-1.16 Å2
2---0.89 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.29→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 0 398 4618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224328
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9435893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51823.857210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7615668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0281530
X-RAY DIFFRACTIONr_chiral_restr0.0960.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213386
X-RAY DIFFRACTIONr_mcbond_it0.6911.52677
X-RAY DIFFRACTIONr_mcangle_it1.25724286
X-RAY DIFFRACTIONr_scbond_it1.96731651
X-RAY DIFFRACTIONr_scangle_it3.034.51607
LS refinement shellResolution: 2.29→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 103 -
Rwork0.227 1749 -
all-1852 -
obs--93.91 %

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