[English] 日本語
Yorodumi- PDB-5tim: REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tim | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX | |||||||||
Components | TRIOSEPHOSPHATE ISOMERASE | |||||||||
Keywords | ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) | |||||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.83 Å | |||||||||
Authors | Wierenga, R.K. / Hol, W.G.J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: Refined 1.83 A structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M-ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate ...Title: Refined 1.83 A structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M-ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex. Authors: Wierenga, R.K. / Noble, M.E. / Vriend, G. / Nauche, S. / Hol, W.G. #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: Proteins / Year: 1991 Title: The Adaptability of the Active Site of Trypanosomal Triosephosphate Isomerase as Observed in the Crystal Structures of Three Different Complexes Authors: Noble, M.E.M. / Wierenga, R.K. / Lambeir, A.-M. / Opperdoes, F.R. / Thunnissen, A.-M.W.H. / Kalk, K.H. / Groendijk, H. / Hol, W.G.J. #3: Journal: J.Med.Chem. / Year: 1991 Title: Crystallographic and Molecular Modeling Studies on Trypanosomal Triosephosphate Isomerase: A Critical Assessment of the Predicted and Observed Structures of the Complex with 2-Phosphoglycerate Authors: Noble, M.E.M. / Verlinde, C.L.M.J. / Groendijk, H. / Kalk, K.H. / Wierenga, R.K. / Hol, W.G.J. #4: 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. #5: 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 |
| |||||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5tim.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5tim.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 5tim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tim_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5tim_full_validation.pdf.gz | 482 KB | Display | |
Data in XML | 5tim_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 5tim_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/5tim ftp://data.pdbj.org/pub/pdb/validation_reports/ti/5tim | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | THE ASYMMETRIC UNIT CONSISTS OF A DIMER. THE TWO MOLECULES HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. SUBUNITS *A* AND *B* DO NOT HAVE IDENTICAL CONFORMATIONS. THE FLEXIBLE LOOP OF SUBUNIT *A* IS OPEN AND THE FLEXIBLE LOOP OF SUBUNIT *B* IS ALMOST CLOSED. THERE IS A SULFATE ION BOUND IN THE ACTIVE SITE OF SUBUNIT *B*. |
-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: Chemical | #3: Chemical | ChemComp-DTT / | #4: Water | ChemComp-HOH / | Compound details | SECONDARY STRUCTURE SPECIFICAT | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: took Wierenga et al.,(1984) from original paper | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 1.83 Å / Lowest resolution: 25 Å / Num. obs: 38819 / Num. measured all: 122216 / Rmerge(I) obs: 0.089 |
---|---|
Reflection shell | *PLUS |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.83→6 Å / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→6 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 37568 / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_d / Dev ideal: 2.9 |