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- PDB-2v2d: The A178L mutation in the C-terminal hinge of the flexible loop-6... -
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Open data
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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 | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL | ||||||
![]() | 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 | ![]() 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 | ![]() ![]() ![]() | ||||||
![]() | Alahuhta, M. / Casteleijn, M.G. / Neubauer, P. / Wierenga, R.K. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 46.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.1 KB | Display | ![]() |
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Full document | ![]() | 440 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v0tC ![]() 2v2cC ![]() 2v2hC ![]() 1ml1S S: Starting model for refinement C: citing same article ( |
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Similar 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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Components
#1: Protein | Mass: 26075.824 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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