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- PDB-2vek: Structure-based enzyme engineering efforts with an inactive monom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vek | ||||||
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Title | Structure-based enzyme engineering efforts with an inactive monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE | ||||||
![]() | ISOMERASE / TRIOSEPHOSPHATE ISOMERASE / TIM BARREL / GLYCOLYSIS / ENGINEERING / PENTOSE SHUNT / BINDING POCKET / GLUCONEOGENESIS / LIPID SYNTHESIS / SUBSTRATE SPECIFICITY / FATTY ACID BIOSYNTHESIS / TIM / ENZYME / MONOMERIC / GLYCOSOME | ||||||
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. / Salin, M. / Casteleijn, M.G. / Kemmer, C. / El-Sayed, I. / Augustyns, K. / Neubauer, P. / Wierenga, R.K. | ||||||
![]() | ![]() Title: Structure-Based Protein Engineering Efforts with a Monomeric Tim Variant: The Importance of a Single Point Mutation for Generating an Active Site with Suitable Binding Properties. Authors: Alahuhta, M. / Salin, M. / Casteleijn, M.G. / Kemmer, C. / El-Sayed, I. / Augustyns, K. / 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. DETERMINATION METHOD: DSSP 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.4 KB | Display | ![]() |
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PDB format | ![]() | 89 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479 KB | Display | ![]() |
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Full document | ![]() | 484.8 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2veiC ![]() 2velC ![]() 2vemC ![]() 2venC ![]() 1dkwS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25659.289 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-13,15-72,80-234,238-250 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-TBU / | #4: Chemical | ChemComp-ASF / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | RESIDUES 14, 72-78, 235-237(THREE RESIDUES DELETED IN LOOP8) IN CHAINS A, B AND C HAVE BEEN REMOVED ...RESIDUES 14, 72-78, 235-237(THREE RESIDUES DELETED IN LOOP8) IN CHAINS A, B AND C HAVE BEEN REMOVED RESULTING IN A DELETION MUTATION OF UNP P04789 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.24 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 20% PEG6000, 2,5% T-BUTANOL, 0.1 M CITRIC ACID PH 5,5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. obs: 56766 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.99 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.27 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DKW Resolution: 1.6→19.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.098 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.087 / 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: 18.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.74 Å
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Refine LS restraints |
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