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Yorodumi- PDB-4ywi: F96S/L167V Double mutant of Plasmodium Falciparum Triosephosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ywi | ||||||
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Title | F96S/L167V Double mutant of Plasmodium Falciparum Triosephosphate Isomerase | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / TIM BARRELS / BETA-ALPHA BARRELS / GLYCOLYSIS | ||||||
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: 1.85 Å | ||||||
Authors | Pareek, V. / Balaram, P. / Murthy, M.R.N. | ||||||
Funding support | India, 1items
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Citation | Journal: Chembiochem / Year: 2016 Title: Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue 96 in the Plasmodial Enzyme Authors: Pareek, V. / Samanta, M. / Joshi, N.V. / Balaram, H. / Murthy, M.R.N. / Balaram, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ywi.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ywi.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ywi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/4ywi ftp://data.pdbj.org/pub/pdb/validation_reports/yw/4ywi | HTTPS FTP |
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-Related structure data
Related structure data | 4x22C 4ymzC 4yxgC 4z0jC 4z0sC 1m7pS 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: 27923.613 Da / Num. of mol.: 2 / Mutation: F96S,A163V,L167V Source method: isolated from a genetically manipulated source Details: MUTATION OF A163V PRESENT IN THE WILD TYPE TIM CONSIDERED AS TEMPLATE Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: TPI / Plasmid: pTrc99A / Details (production host): PARC1008 / Production host: Escherichia coli (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, triose-phosphate isomerase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 1450 22%, HEPES, Li2SO4 10mM, DTT 0.5mM, NaN3 0.5mM, EDTA 0.5mM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50.93 Å / Num. obs: 35109 / % possible obs: 83.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 38 |
Reflection shell | Resolution: 1.85→1.94 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 12.8 / % possible all: 61.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M7P Resolution: 1.85→33.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.6 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.031 / 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: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→33.89 Å
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Refine LS restraints |
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