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Yorodumi- PDB-2vfi: Crystal structure of the Plasmodium falciparum triosephosphate is... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vfi | ||||||
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Title | Crystal structure of the Plasmodium falciparum triosephosphate isomerase in the loop closed state with 3-phosphoglycerate bound at the active site and interface | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE / PLASMODIUM FALCIPARUM / FATTY ACID BIOSYNTHESIS / TRIOSEPHOSPHATE ISOMERASE / TIM / MUTANT / GLYCOLYSIS / LOOP CLOSED / PENTOSE SHUNT / GLUCONEOGENESIS / LIPID SYNTHESIS | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / identical protein binding Similarity search - Function | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Gayathri, P. / Banerjee, M. / Vijayalakshmi, A. / Balaram, H. / Balaram, P. / Murthy, M.R.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vfi.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vfi.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/2vfi ftp://data.pdbj.org/pub/pdb/validation_reports/vf/2vfi | HTTPS FTP |
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-Related structure data
Related structure data | 2vfdC 2vfeC 2vffC 2vfgC 2vfhC 1o5xS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.314658, 0.307135, -0.898142), Vector: |
-Components
#1: Protein | Mass: 27997.738 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Plasmid: PARC1008 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, triose-phosphate isomerase #2: Chemical | ChemComp-3PG / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 2006 / Details: OSMIC MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 22598 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 1.82 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 80.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O5X Resolution: 2.25→91.29 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.88 / SU B: 8.143 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.493 / ESU R Free: 0.272 / 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: 22.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→91.29 Å
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