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- PDB-3hzu: Crystal structure of probable thiosulfate sulfurtransferase SSEA ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hzu | ||||||
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Title | Crystal structure of probable thiosulfate sulfurtransferase SSEA (rhodanese) from Mycobacterium tuberculosis | ||||||
![]() | Thiosulfate sulfurtransferase sseA | ||||||
![]() | TRANSFERASE / NIAID / SSGCID / Infectious Disease / tuberculosis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() thiosulfate sulfurtransferase / thiosulfate sulfurtransferase activity / cell wall / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.2 KB | Display | ![]() |
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PDB format | ![]() | 55 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445 KB | Display | ![]() |
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Full document | ![]() | 445.7 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3p3aC ![]() 1uarS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35649.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P96888, UniProt: P9WHF7*PLUS, thiosulfate sulfurtransferase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.52 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.22 Å2 / Biso mean: 33.71 Å2 / Biso min: 19.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→31.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.151 Å / Total num. of bins used: 20
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