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- PDB-7rgc: Crystal structure of triosephosphate isomerase from Candidatus Ab... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rgc | ||||||
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Title | Crystal structure of triosephosphate isomerase from Candidatus Absconditabacteria (Sr1) bacterium | ||||||
![]() | 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. / Compton, J. / Fraga, D. / Patrick, W.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Sr1TPI - Candidatus Absconditabacteria bacterium triosephoshate isomerase Authors: Vickers, C.J. / Fraga, D. / Compton, J. / Patrick, W.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126 KB | Display | ![]() |
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PDB format | ![]() | 78.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.1 KB | Display | ![]() |
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Full document | ![]() | 444.2 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 26.5 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27606.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: tpiA, P148_SR1C00001G0257 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.49 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 2.3 M DL-Malic acid pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→45.82 Å / Num. obs: 30881 / % possible obs: 99.2 % / Redundancy: 20.3 % / Biso Wilson estimate: 31.73 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.74 |
Reflection shell | Resolution: 2.09→2.22 Å / Num. unique obs: 4732 / CC1/2: 0.83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1b9b Resolution: 2.09→44 Å / SU ML: 0.2863 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.405 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: 47.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→44 Å
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Refine LS restraints |
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LS refinement shell |
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