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- PDB-3hzu: Crystal structure of probable thiosulfate sulfurtransferase SSEA ... -

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Basic information

Entry
Database: PDB / ID: 3hzu
TitleCrystal structure of probable thiosulfate sulfurtransferase SSEA (rhodanese) from Mycobacterium tuberculosis
ComponentsThiosulfate sulfurtransferase sseA
KeywordsTRANSFERASE / NIAID / SSGCID / Infectious Disease / tuberculosis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


thiosulfate sulfurtransferase / cell wall / thiosulfate sulfurtransferase activity / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
: / Rhodanese signature 1. / 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 signature 1. / 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 SseA / Putative thiosulfate sulfurtransferase SseA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Protein Sci. / Year: 2012
Title: Mycobacterium thermoresistibile as a source of thermostable orthologs of Mycobacterium tuberculosis proteins.
Authors: Edwards, T.E. / Liao, R. / Phan, I. / Myler, P.J. / Grundner, C.
#1: Journal: 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 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Apr 22, 2015Group: Database references
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiosulfate sulfurtransferase sseA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8383
Polymers35,6501
Non-polymers1882
Water2,792155
1
A: Thiosulfate sulfurtransferase sseA
hetero molecules

A: Thiosulfate sulfurtransferase sseA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6766
Polymers71,3002
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area2940 Å2
ΔGint-22 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.730, 88.327, 36.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Thiosulfate sulfurtransferase sseA


Mass: 35649.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: sseA, Rv3283, MT3382, MTCY71.23 / Production host: Escherichia coli (E. coli)
References: UniProt: P96888, UniProt: P9WHF7*PLUS, thiosulfate sulfurtransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.4 M ammonium sulfate, 0.1 M BisTris pH 6.5, 36.6 mg/mL protein, crystal ID 203314g9, 15% glycerol as cryo-protectant, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 18019 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.084 / Χ2: 1.02 / Net I/σ(I): 16.649
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1704 / Χ2: 0.948 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.33 Å31.78 Å
Translation2.33 Å31.78 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: 2.1→31.81 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.821 / SU B: 5.235 / SU ML: 0.141 / SU R Cruickshank DPI: 0.259 / SU Rfree: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 914 5.1 %RANDOM
Rwork0.205 ---
obs0.208 17967 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.22 Å2 / Biso mean: 33.71 Å2 / Biso min: 19.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20 Å2
2---2.78 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 11 155 2460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212390
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9413274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4185295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.35922.783115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80415346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1341522
X-RAY DIFFRACTIONr_chiral_restr0.0720.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211885
X-RAY DIFFRACTIONr_mcbond_it0.4711.51467
X-RAY DIFFRACTIONr_mcangle_it0.87522367
X-RAY DIFFRACTIONr_scbond_it1.1483923
X-RAY DIFFRACTIONr_scangle_it1.8854.5907
LS refinement shellResolution: 2.1→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 66 -
Rwork0.246 1197 -
all-1263 -
obs--95.83 %

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