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Yorodumi- PDB-1tpd: STRUCTURES OF THE "OPEN" AND "CLOSED" STATE OF TRYPANOSOMAL TRIOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tpd | ||||||
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Title | STRUCTURES OF THE "OPEN" AND "CLOSED" STATE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, AS OBSERVED IN A NEW CRYSTAL FORM: IMPLICATIONS FOR THE REACTION MECHANISM | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) | ||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Noble, M.E.M. / Zeelen, J.Ph. / Wierenga, R.K. | ||||||
Citation | Journal: Proteins / Year: 1993 Title: Structures of the "open" and "closed" state of trypanosomal triosephosphate isomerase, as observed in a new crystal form: implications for the reaction mechanism. Authors: Noble, M.E. / Zeelen, J.P. / 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 | 1tpd.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tpd.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/1tpd ftp://data.pdbj.org/pub/pdb/validation_reports/tp/1tpd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26865.832 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: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.19 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 7.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 26860 / % possible obs: 78 % / Num. measured all: 59116 / Rmerge(I) obs: 0.063 |
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Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.13 Å / % possible obs: 57.6 % |
-Processing
Software |
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Refinement | Highest resolution: 2.1 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection all: 26879 / Rfactor all: 0.176 / Rfactor Rwork: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.46 |