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Yorodumi- PDB-1tsi: STRUCTURE OF THE COMPLEX BETWEEN TRYPANOSOMAL TRIOSEPHOSPHATE ISO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tsi | ||||||
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Title | STRUCTURE OF THE COMPLEX BETWEEN TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE AND N-HYDROXY-4-PHOSPHONO-BUTANAMIDE: BINDING AT THE ACTIVE SITE DESPITE AN "OPEN" FLEXIBLE LOOP | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.84 Å | ||||||
Authors | Verlinde, C.L.M.J. | ||||||
Citation | Journal: Protein Sci. / Year: 1992 Title: Structure of the complex between trypanosomal triosephosphate isomerase and N-hydroxy-4-phosphono-butanamide: binding at the active site despite an "open" flexible loop conformation. Authors: Verlinde, C.L. / Witmans, C.J. / Pijning, T. / Kalk, K.H. / Hol, W.G. / Callens, M. / Opperdoes, F.R. #1: Journal: Proteins / Year: 1991 Title: The Crystal Structure of the "Open" and the "Closed" Conformation of the Flexible Loop of Trypanosomal Triosephosphate Isomerase Authors: Wierenga, R.K. / Noble, M.E.M. / Postma, J.P.M. / Groendijk, H. / Kalk, K.H. / Hol, W.G.J. / Opperdoes, F.R. #2: Journal: J.Mol.Biol. / Year: 1987 Title: Structure Determination of the Glycosomal Triosephosphate Isomerase from Trypanosoma Brucei Brucei at 2.4 Angstroms Resolution Authors: Wierenga, R.K. / Kalk, K.H. / Hol, W.G.J. #3: Journal: J.Mol.Biol. / Year: 1984 Title: Preliminary Crystallographic Studies of Triosephosphate Isomerase from the Blood Parasite Trypanosoma Brucei Brucei Authors: Wierenga, R.K. / Hol, W.G.J. / Misset, O. / Opperdoes, F.R. | ||||||
History |
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Remark 700 | SHEET THE SHEETS PRESENTED AS *A* AND *B* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *A* AND *B* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tsi.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tsi.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/1tsi ftp://data.pdbj.org/pub/pdb/validation_reports/ts/1tsi | 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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Details | THE ASYMMETRIC UNIT CONSISTS OF A DIMER. THE TWO MOLECULES HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. THE CRYSTALS USED FOR THIS STRUCTURE DETERMINATION WERE GROWN IN THE PRESENCE OF 2.4M AMMONIUM SULFATE (SEE PROTEIN DATA BANK ENTRY 2TIM), BUT BEFORE DATA COLLECTION THESE CRYSTALS WERE TRANSFERRED TO A MOTHER LIQUOR WITHOUT SULFATE. THE ACTIVE SITE OF SUBUNIT *A* CONTAINS THE INHIBITOR N-HYDROXY-4-PHOSPHONO-BUTANAMIDE (KI = 0.3 * 10**-3 M). IN THIS ENTRY THE FLEXIBLE LOOP (LOOP 6) OF EACH SUBUNIT IS IN AN OPEN CONFORMATION. |
-Components
#1: Protein | Mass: 26951.947 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | ChemComp-4PB / | #3: Water | ChemComp-HOH / | Compound details | SECONDARY STRUCTURE SPECIFICAT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.13 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.84 Å / Num. obs: 6530 / % possible obs: 95.8 % / Rmerge(I) obs: 0.063 |
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-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.84→6 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.84→6 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.115 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 3.5 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_d / Dev ideal: 3.2 |