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- PDB-7rcq: Crystal structure of triosephosphate isomerase from Ktedonobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rcq | ||||||
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Title | Crystal structure of triosephosphate isomerase from Ktedonobacter racemifer | ||||||
![]() | 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 Ktedonobacter racemifer 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 | ![]() | 80.6 KB | Display | ![]() |
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PDB format | ![]() | 46.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y8fS 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: 29076.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.25 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium nitrate, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5406 Å |
Detector | Type: AGILENT TITAN CCD / Detector: CCD / Date: Jul 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→13.18 Å / Num. obs: 25558 / % possible obs: 98.2 % / Redundancy: 3 % / Biso Wilson estimate: 10.33 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 1282 / CC1/2: 0.972 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4y8f Resolution: 1.7→13.18 Å / SU ML: 0.1574 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.776 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: 12.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→13.18 Å
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Refine LS restraints |
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LS refinement shell |
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