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Yorodumi- PDB-2v2d: The A178L mutation in the C-terminal hinge of the flexible loop-6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2d | ||||||
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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 / ENGINEERING / PENTOSE SHUNT / POINT MUTATION / TIM / A178L / LOOP6 / HINGE / LOOP-6 / ENZYME / FATTY ACID BIOSYNTHESIS / TRIOSEPHOSPHATE ISOMERASE / GLYCOSOME / MONOMERIC / TIM-BARREL / GLYCOLYSIS | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v2d.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2d.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 2v2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2d ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2d | HTTPS FTP |
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-Related structure data
Related structure data | 2v0tC 2v2cC 2v2hC 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.: 1 / 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 |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.02 % / Description: NONE |
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Crystal grow | pH: 8.2 / Details: 1.75 M (NH4)2PO4, PH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.847 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 26, 2004 / Details: FLAT PRE-MIRROR AND BENT, VERTICALLY FOCUSSING |
Radiation | Monochromator: SI 111, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.847 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 11321 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 12.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.45 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 12.44 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 13.03 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ML1 Resolution: 2.3→19.22 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.951 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.22 Å
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Refine LS restraints |
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