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- PDB-6tim: THE ADAPTABILITY OF THE ACTIVE SITE OF TRYPANOSOMAL TRIOSEPHOSPHA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tim | ||||||
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Title | THE ADAPTABILITY OF THE ACTIVE SITE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE AS OBSERVED IN THE CRYSTAL STRUCTURES OF THREE DIFFERENT COMPLEXES | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE | ||||||
![]() | ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Noble, M.E.M. / Wierenga, R.K. / Hol, W.G.J. | ||||||
![]() | ![]() 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. / Wierenga, R.K. / Lambeir, A.M. / Opperdoes, F.R. / Thunnissen, A.M. / Kalk, K.H. / Groendijk, H. / Hol, W.G. #1: ![]() 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 ...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 Authors: Wierenga, R.K. / Noble, M.E.M. / Vriend, G. / Nauche, S. / Hol, W.G.J. #2: ![]() 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. #3: ![]() 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: ![]() 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: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.9 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399.4 KB | Display | ![]() |
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Full document | ![]() | 413 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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*. 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 CLOSED. GLYCEROL-3-PHOSPHATE IS BOUND IN THE ACTIVE SITE OF SUBUNIT *B*. |
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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.) ![]() ![]() #2: Chemical | ChemComp-G3P / | #3: Water | ChemComp-HOH / | Compound details | SECONDARY STRUCTURE SPECIFICAT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.31 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Details: THIS STRUCTURE IS OBTAINED FROM CRYSTALS GROWN IN 2.4M AMMONIUM SULPHATE AND TRANSFERRED INTO SULPHATE FREE MOTHER LIQUOR CONTAINING 6MM DL-GLYCEROL-3-PHOSPHATE. | ||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.2 Å / Num. obs: 18064 / Rmerge(I) obs: 0.043 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→50 Å /
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. reflection obs: 16881 / Rfactor obs: 0.137 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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