+Open data
-Basic information
Entry | Database: PDB / ID: 1i45 | ||||||
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Title | YEAST TRIOSEPHOSPHATE ISOMERASE (MUTANT) | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE / TRIOSEPHOSPHATE ISOMERASE / mutant / yeast / 5'-fluorotryptophan | ||||||
Function / homology | Function and homology information Gluconeogenesis / Glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane ...Gluconeogenesis / Glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Rozovsky, S. / Jogl, G. / Tong, L. / McDermott, A.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Solution-state NMR investigations of triosephosphate isomerase active site loop motion: ligand release in relation to active site loop dynamics. Authors: Rozovsky, S. / Jogl, G. / Tong, L. / McDermott, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i45.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i45.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/1i45 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/1i45 | HTTPS FTP |
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-Related structure data
Related structure data | 1ypiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26783.342 Da / Num. of mol.: 2 / Mutation: TRP90TYR, TRP157PHE, TRP168FTR Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JA300 / References: UniProt: P00942, triose-phosphate isomerase #2: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54.47 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: batch / pH: 6.8 Details: 16% PEG 4000, 50mM Tris, 50mM NaCl, pH 6.8, batch at 293 K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 50358 / Num. obs: 50343 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 44.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.305 / % possible all: 82.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 50459 / Num. measured all: 152637 / Rmerge(I) obs: 0.073 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1ypi Resolution: 1.8→29.75 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 329070.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.8 Å2 / ksol: 0.318 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 50392 / σ(F): 0 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.308 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.282 |