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Yorodumi- PDB-2v2c: The A178L mutation in the C-terminal hinge of the flexible loop-6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2c | |||||||||
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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 / GLYCOSOME / TIM-BARREL / GLYCOLYSIS / ENGINEERING / PENTOSE SHUNT / POINT MUTATION / TIM / 2PG / A178L / LOOP6 / HINGE / LOOP-6 / ENZYME / FATTY ACID BIOSYNTHESIS / TRIOSEPHOSPHATE ISOMERASE / GLUCONEOGENESIS / LIPID SYNTHESIS / 2-PHOSPHO GLYCOLLATE | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.89 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 | 2v2c.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2c.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 2v2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v2c_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 2v2c_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 2v2c_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 2v2c_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2c ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2c | HTTPS FTP |
-Related structure data
Related structure data | 2v0tC 2v2dC 2v2hC 5timS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26907.912 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 | #3: Chemical | ChemComp-PGA / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.96 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M TEA PH 7.5, 2 % PEG 400, 2.0 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 28, 2005 / Details: MONTEL MIRRORS |
Radiation | Monochromator: MONTEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→25 Å / Num. obs: 27265 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 8.52 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 63.26 |
Reflection shell | Resolution: 1.89→1.95 Å / Redundancy: 6.05 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 26.98 / % possible all: 95.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5TIM Resolution: 1.89→20.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.165 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→20.01 Å
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Refine LS restraints |
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