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Yorodumi- PDB-1if2: X-RAY STRUCTURE OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1if2 | ||||||
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Title | X-RAY STRUCTURE OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE COMPLEXED WITH IPP | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE / TIM barrel / transition state analogue | ||||||
Function / homology | Function and homology information glycosome / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kursula, I. / Partanen, S. / Lambeir, A.-M. / Antonov, D.M. / Augustyns, K. / Wierenga, R.K. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2001 Title: Structural determinants for ligand binding and catalysis of triosephosphate isomerase. Authors: Kursula, I. / Partanen, S. / Lambeir, A.M. / Antonov, D.M. / Augustyns, K. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1if2.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1if2.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 1if2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1if2 ftp://data.pdbj.org/pub/pdb/validation_reports/if/1if2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: E65Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (eukaryote) / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P48499, triose-phosphate isomerase |
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#2: Chemical | ChemComp-129 / [ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.89 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 6000, CH3COOH/NaOH, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 26, 2000 / Details: mirrors |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 18318 / Num. obs: 18318 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 9.3 / Num. unique all: 1843 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 74174 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22.2 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.16 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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