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Yorodumi- PDB-2v2h: The A178L mutation in the C-terminal hinge of the flexible loop-6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2h | |||||||||
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Title | The A178L mutation in the C-terminal hinge of the flexible loop-6 of triosephosphate isomerase (TIM) induces a more closed conformation of this hinge region in dimeric and monomeric TIM | |||||||||
Components | TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL | |||||||||
Keywords | ISOMERASE / GLUCONEOGENESIS / LIPID SYNTHESIS / 2-PHOSPHO GLYCOLATE / GLYCOLYSIS / ENGINEERING / PENTOSE SHUNT / POINT MUTATION / TIM / 2PG / A178L / LOOP6 / HINGE / LOOP-6 / ENZYME / FATTY ACID BIOSYNTHESIS / TRIOSEPHOSPHATE ISOMERASE / GLYCOSOME / MONOMERIC / TIM-BARREL | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | |||||||||
Authors | Alahuhta, M. / Casteleijn, M.G. / Neubauer, P. / Wierenga, R.K. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structural Studies Show that the A178L Mutation in the C-Terminal Hinge of the Catalytic Loop-6 of Triosephosphate Isomerase (Tim) Induces a Closed-Like Conformation in Dimeric and Monomeric Tim. Authors: Alahuhta, M. / Casteleijn, M.G. / Neubauer, P. / Wierenga, R.K. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET 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 | 2v2h.cif.gz | 317.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2h.ent.gz | 258.8 KB | Display | PDB format |
PDBx/mmJSON format | 2v2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2h ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2h | HTTPS FTP |
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-Related structure data
Related structure data | 2v0tC 2v2cC 2v2dC 1ml1S S: Starting model for refinement C: citing same article (ref.) |
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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: 26075.824 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ALA 178 TO LEU ENGINEERED RESIDUE IN CHAIN B, ALA 178 TO LEU ...ENGINEERED | |
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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: 2.2 Å3/Da / Density % sol: 43.2 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.1 M CITRIC ACID PH 5.5, 20% PEG 6K, 3% TERT.BUTANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.793 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 30, 2005 / Details: RH COATED, ZERODUR |
Radiation | Monochromator: FIXED EXIT DOUBLE CRYSTAL SI 111, HORIZONTALLY FOCUSSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.793 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→25 Å / Num. obs: 210261 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.01 |
Reflection shell | Resolution: 1.18→1.19 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ML1 Resolution: 1.18→25 Å / Num. restraintsaints: 69700 / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6357.69 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→25 Å
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Refine LS restraints |
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