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Yorodumi- PDB-1ci1: CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM TRYPANOSOMA C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ci1 | ||||||
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Title | CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM TRYPANOSOMA CRUZI IN HEXANE | ||||||
Components | PROTEIN (TRIOSEPHOSPHATE ISOMERASE) | ||||||
Keywords | TRIOSEPHOSPHATE ISOMERASE / TRYPANOSOMA CRUZI / ORGANIC SOLVENT / HEXANE / OLIGOMERIC PROTEIN | ||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2 Å | ||||||
Authors | Gao, X.-G. / Maldondo, E. / Perez-Montfort, R. / De Gomez-Puyou, M.T. / Gomez-Puyou, A. / Rodriguez-Romero, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane. Authors: Gao, X.G. / Maldonado, E. / Perez-Montfort, R. / Garza-Ramos, G. / de Gomez-Puyou, M.T. / Gomez-Puyou, A. / Rodriguez-Romero, A. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Differences in the intersubunit contacts in triosephosphate isomerase from two closely related pathogenic trypanosomes. Authors: Maldonado, E. / Soriano-Garcia, M. / Moreno, A. / Cabrera, N. / Garza-Ramos, G. / de Gomez-Puyou, M. / Gomez-Puyou, A. / Perez-Montfort, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ci1.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ci1.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ci1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/1ci1 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/1ci1 | HTTPS FTP |
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-Related structure data
Related structure data | 1tcdS 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: 27360.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: MEXICAN NINOA STRAIN / Plasmid: PET23A / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL23(DE3) / References: UniProt: P52270, triose-phosphate isomerase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE FIRST 3 N-TERMINAL RESIDUE WERE NOT BUILT INTO THE MODEL A AS THEY WERE NOT SEEEN IN THE ...THE FIRST 3 N-TERMINAL RESIDUE WERE NOT BUILT INTO THE MODEL A AS THEY WERE NOT SEEEN IN THE DENSITY MAPS THE FIRST 2 N-TERMINAL RESIDUE WERE NOT BUILT INTO THE MODEL B AS THEY WERE NOT SEEN IN THE DENSITY MAPS | |
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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: 2.32 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED AT ROOM TEMPERATUTE BY VAPER DIFFUSION FROM 0.1 M NA HEPES PH7.5, 2%(V/V) PEG400 AND 2.0 M AMMONIUM SULFATE, THEN SOAKED IN ANHYDROUS N-HEXANE. , VAPOR DIFFUSION | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 21, 1998 / 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: 1.95→25 Å / Num. obs: 31766 / % possible obs: 84.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 4.64 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 2.1 / % possible all: 65.5 |
Reflection | *PLUS Num. measured all: 172135 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1TCD Resolution: 2→5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 5 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.358 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.309 |