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- PDB-7r9b: Crystal structure of Triosephosphate isomerase from Candidatus Ro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r9b | ||||||
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Title | Crystal structure of Triosephosphate isomerase from Candidatus Roizmanbacteria | ||||||
![]() | Triosephosphate isomerase | ||||||
![]() | ISOMERASE / TIM / triosephosphate isomerase / glycolysis / gluconeogenesis | ||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vickers, C.J. / Patrick, W.M. / Fraga, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Triosephosphate isomerase from Candidatus Roizmanbacteria Authors: Vickers, C.J. / Patrick, W.M. / Fraga, 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 | ![]() | 68.8 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.2 KB | Display | ![]() |
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Full document | ![]() | 815.1 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yyaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 24678.947 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.79 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M phosphate/citrate pH 4.2, 40% v/v PEG 300. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→41.01 Å / Num. obs: 14485 / % possible obs: 99.8 % / Redundancy: 20.5 % / Biso Wilson estimate: 39.87 Å2 / CC1/2: 1 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Num. unique obs: 1205 / CC1/2: 0.953 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YYA Resolution: 2.2→37.61 Å / SU ML: 0.2569 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1243 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→37.61 Å
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Refine LS restraints |
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LS refinement shell |
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