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- PDB-1urh: The "Rhodanese" fold and catalytic mechanism of 3-mercaptopyruvat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1urh | ||||||
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Title | The "Rhodanese" fold and catalytic mechanism of 3-mercaptopyruvate sulfotransferases: Crystal structure of SseA from Escherichia coli | ||||||
![]() | 3-MERCAPTOPYRUVATE SULFURTRANSFERASE | ||||||
![]() | TRANSFERASE / SULFUR-TRANSFERASE / RHODANESE | ||||||
Function / homology | ![]() 3-mercaptopyruvate sulfurtransferase / 3-mercaptopyruvate sulfurtransferase activity / thiosulfate sulfurtransferase activity / DNA protection / transsulfuration / response to oxidative stress / response to antibiotic / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Spallarossa, A. / Forlani, F. / Carpen, A. / Armirotti, A. / Pagani, S. / Bolognesi, M. / Bordo, D. | ||||||
![]() | ![]() Title: The "Rhodanese" Fold and Catalytic Mechanism of 3-Mercaptopyruvate Sulfurtransferases: Crystal Structure of Ssea from Escherichia Coli Authors: Spallarossa, A. / Forlani, F. / Carpen, A. / Armirotti, A. / Pagani, S. / Bolognesi, M. / Bordo, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112 KB | Display | ![]() |
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PDB format | ![]() | 86.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.1 KB | Display | ![]() |
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Full document | ![]() | 475.6 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rhsS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30741.596 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RESIDUES A186-A189 AND B181-B191 ARE NOT INCLUDED IN THE MODEL. Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P31142, 3-mercaptopyruvate sulfurtransferase #2: Chemical | ChemComp-SO3 / | #3: Water | ChemComp-HOH / | Compound details | 3-MERCAPTOPY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K / pH: 8 / Method: vapor diffusion, hanging drop / Details: Spallarossa, A., (2003) Acta Cryst., D59, 168. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Jul 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 21524 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 14 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2 / % possible all: 97.9 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 40 Å / % possible obs: 95.6 % / Num. measured all: 312079 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 97.9 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RHS Resolution: 2.8→40 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.8→40 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.447 / Rfactor Rwork: 0.385 |