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- PDB-7n8u: Crystal structure of Triosephosphate isomerase from Candidatus Pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n8u | ||||||
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Title | Crystal structure of Triosephosphate isomerase from Candidatus Prometheoarchaeum syntrophicum | ||||||
![]() | 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: Structure of PsyTPI - Candidatus Prometheoarchaeum syntrophicum triosephosphate isomerase. 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 | ![]() | 148.2 KB | Display | ![]() |
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PDB format | ![]() | 91.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.6 KB | Display | ![]() |
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Full document | ![]() | 422.7 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 37.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b9bS 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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Unit cell |
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Components
#1: Protein | Mass: 29099.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: tpiA, DSAG12_02076 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | The sequence annotated as insertion is actually the actual start site of the gene. It is not ...The sequence annotated as insertion is actually the actual start site of the gene. It is not present in the UniProt sequence used for the sequence reference. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.32 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 25 % v/v Polyethylene glycol monomethyl ether 550, 50 mM HEPES; pH 7.0, 10 mM Magnesium chloride |
-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: 1.98→44.24 Å / Num. obs: 43128 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 25.22 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.98→2.1 Å / Num. unique obs: 6790 / CC1/2: 0.921 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1B9B Resolution: 1.98→44.24 Å / SU ML: 0.1492 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.0693 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: 28.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→44.24 Å
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Refine LS restraints |
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LS refinement shell |
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