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- PDB-7pej: Crystal structure of Triosephosphate Isomerase from Schizosacchar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pej | ||||||
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Title | Crystal structure of Triosephosphate Isomerase from Schizosaccharomyces pombe (SpTIM wt) | ||||||
![]() | Triosephosphate isomerase | ||||||
![]() | ISOMERASE / TIM / TIM barrel / Glycolytic enzyme | ||||||
Function / homology | ![]() Glycolysis / Gluconeogenesis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / canonical glycolysis / glycerol catabolic process / gluconeogenesis / glycolytic process / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Romero-Romero, S. / Garza-Ramos, G. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of Triosephosphate Isomerase from Schizosaccharomyces pombe (SpTIM wt) Authors: Romero-Romero, S. / Garza-Ramos, G. #1: ![]() Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 488.9 KB | Display | ![]() |
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PDB format | ![]() | 337.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ff7S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27129.814 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: tpi1, tpi, SPCC24B10.21 / Plasmid: pET24a(+) / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.9 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 2.2 M Ammonium sulphate, 0.2 M Lithium acetate, 9.1 mg/mL protein concentration |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 20, 2021 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→37.38 Å / Num. obs: 103063 / % possible obs: 99.77 % / Redundancy: 7.6 % / Biso Wilson estimate: 36.36 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09633 / Rpim(I) all: 0.03754 / Rrim(I) all: 0.1035 / Net I/σ(I): 13.11 |
Reflection shell | Resolution: 1.79→1.854 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.437 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 10149 / CC1/2: 0.307 / CC star: 0.64 / Rpim(I) all: 0.9385 / Rrim(I) all: 0.915 / % possible all: 98.26 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FF7 Resolution: 1.79→37.38 Å / SU ML: 0.3221 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1053 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: 40.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→37.38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.1488993668 Å / Origin y: 32.0074573593 Å / Origin z: -34.1968980036 Å
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Refinement TLS group | Selection details: all |