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Yorodumi- PDB-5vwn: Triosephosphate isomerases deletion loop 3 from Trichomonas vaginalis -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vwn | ||||||
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Title | Triosephosphate isomerases deletion loop 3 from Trichomonas vaginalis | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / loop deletion | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | Trichomonas vaginalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å | ||||||
Authors | Lara-Gonzalez, S. / Rojas-Mendez, K. / Jimenez-Sandoval, P. / Estrella-Hernandez, P. / Brieba, L.G. | ||||||
Funding support | Mexico, 1items
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Citation | Journal: Biochim. Biophys. Acta / Year: 2017 Title: A competent catalytic active site is necessary for substrate induced dimer assembly in triosephosphate isomerase. Authors: Jimenez-Sandoval, P. / Vique-Sanchez, J.L. / Hidalgo, M.L. / Velazquez-Juarez, G. / Diaz-Quezada, C. / Arroyo-Navarro, L.F. / Moran, G.M. / Fattori, J. / Jessica Diaz-Salazar, A. / Rudino- ...Authors: Jimenez-Sandoval, P. / Vique-Sanchez, J.L. / Hidalgo, M.L. / Velazquez-Juarez, G. / Diaz-Quezada, C. / Arroyo-Navarro, L.F. / Moran, G.M. / Fattori, J. / Jessica Diaz-Salazar, A. / Rudino-Pinera, E. / Sotelo-Mundo, R. / Figueira, A.C.M. / Lara-Gonzalez, S. / Benitez-Cardoza, C.G. / Brieba, L.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vwn.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vwn.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 5vwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/5vwn ftp://data.pdbj.org/pub/pdb/validation_reports/vw/5vwn | HTTPS FTP |
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-Related structure data
Related structure data | 4wjeS 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
#1: Protein | Mass: 26842.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_096350 / Production host: Escherichia coli (E. coli) / References: UniProt: A2FT29, triose-phosphate isomerase |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.14 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.2 M Calcium Acetate, 0.1 M Sodium Cacodylate pH 6.5, 18 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å | |||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 15, 2011 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.74→52.44 Å / Num. obs: 29766 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 20.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.03 / Rrim(I) all: 0.063 / Net I/σ(I): 12.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WJE Resolution: 1.74→38.601 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.21 Å2 / Biso mean: 21.0969 Å2 / Biso min: 9.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.74→38.601 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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