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- PDB-2vfd: Crystal structure of the F96S mutant of Plasmodium falciparum tri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vfd | ||||||
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Title | Crystal structure of the F96S mutant of Plasmodium falciparum triosephosphate isomerase | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE | ||||||
![]() | ISOMERASE / PLASMODIUM FALCIPARUM / FATTY ACID BIOSYNTHESIS / TRIOSEPHOSPHATE ISOMERASE / PENTOSE SHUNT / GLUCONEOGENESIS / LIPID SYNTHESIS / TIM / MUTANT / LOOP OPEN / GLYCOLYSIS | ||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gayathri, P. / Banerjee, M. / Vijayalakshmi, A. / Balaram, H. / Balaram, P. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Biochemical and Structural Characterization of Residue 96 Mutants of Plasmodium Falciparum Triosephosphate Isomerase: Active-Site Loop Conformation, Hydration and Identification of a Dimer- ...Title: Biochemical and Structural Characterization of Residue 96 Mutants of Plasmodium Falciparum Triosephosphate Isomerase: Active-Site Loop Conformation, Hydration and Identification of a Dimer-Interface Ligand-Binding Site. Authors: Gayathri, P. / Banerjee, M. / Vijayalakshmi, A. / Balaram, H. / Balaram, P. / Murthy, M.R.N. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.8 KB | Display | ![]() |
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PDB format | ![]() | 95.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.7 KB | Display | ![]() |
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Full document | ![]() | 438.2 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vfeC ![]() 2vffC ![]() 2vfgC ![]() 2vfhC ![]() 2vfiC ![]() 1o5xS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.312775, 0.294071, 0.903158), Vector: |
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Components
#1: Protein | Mass: 27937.641 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MUTATION OF V163A PRESENT IN THE WILD TYPE TIM CONSIDERED AS TEMPLATE Source: (gene. exp.) ![]() ![]() Plasmid: PARC1008 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, PHE 96 TO SER ENGINEERED RESIDUE IN CHAIN B, PHE 96 TO SER ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 43.8 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 0.1 M SODIUM ACETATE PH 4.0-5.5, PEG 1450 8-24% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DIP-2040B / Detector: IMAGE PLATE / Date: Mar 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 90838 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 7 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1O5X Resolution: 1.4→36.76 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.882 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.788 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→36.76 Å
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Refine LS restraints |
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