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Yorodumi- PDB-7pek: Crystal structure of Triosephosphate Isomerase C216A mutant from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pek | ||||||
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Title | Crystal structure of Triosephosphate Isomerase C216A mutant from Schizosaccharomyces pombe (SpTIM C216A) | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / TIM / TIM barrel / Glycolytic enzyme | ||||||
Function / homology | Function and homology information 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 | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Romero-Romero, S. / Garza-Ramos, G. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of Triosephosphate Isomerase from Schizosaccharomyces pombe (SpTIM C216A) Authors: Romero-Romero, S. / Garza-Ramos, G. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pek.cif.gz | 493.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pek.ent.gz | 339 KB | Display | PDB format |
PDBx/mmJSON format | 7pek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pek_validation.pdf.gz | 486.5 KB | Display | wwPDB validaton report |
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Full document | 7pek_full_validation.pdf.gz | 498.7 KB | Display | |
Data in XML | 7pek_validation.xml.gz | 45.3 KB | Display | |
Data in CIF | 7pek_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/7pek ftp://data.pdbj.org/pub/pdb/validation_reports/pe/7pek | HTTPS FTP |
-Related structure data
Related structure data | 4ff7S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 27097.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: C216A mutation Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: tpi1, tpi, SPCC24B10.21 / Plasmid: pET24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07669, triose-phosphate isomerase |
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-Non-polymers , 5 types, 894 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 2.4 M Ammonium sulphate, 0.1 M Bicine pH:9.0, 11.1 mg/mL protein concentration |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
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: 1.74→47.12 Å / Num. obs: 110326 / % possible obs: 99.69 % / Redundancy: 7.6 % / Biso Wilson estimate: 33.62 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09564 / Rpim(I) all: 0.03707 / Rrim(I) all: 0.1027 / Net I/σ(I): 13.49 |
Reflection shell | Resolution: 1.74→1.806 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 10711 / CC1/2: 0.312 / CC star: 0.654 / Rpim(I) all: 0.8809 / Rrim(I) all: 0.912 / % possible all: 97.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FF7 Resolution: 1.74→47.12 Å / SU ML: 0.2408 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7494 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: 40.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→47.12 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: -31.9728917254 Å / Origin y: -15.0552597992 Å / Origin z: 34.9495210898 Å
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Refinement TLS group | Selection details: all |