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Yorodumi- PDB-5upr: X-ray structure of a putative triosephosphate isomerase from Toxo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5upr | ||||||
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Title | X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49 | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Cardona-Correa, A. / Bishop, B. / Anderson, W.F. / Ngo, H. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49 Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Cardona-Correa, A. / Bishop, B. / Anderson, W.F. / Ngo, H. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5upr.cif.gz | 414.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5upr.ent.gz | 354 KB | Display | PDB format |
PDBx/mmJSON format | 5upr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/5upr ftp://data.pdbj.org/pub/pdb/validation_reports/up/5upr | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 28399.596 Da / Num. of mol.: 4 / Fragment: UNP residues 111-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote) Strain: ATCC 50611 / Me49 / Gene: TPI-II, TGME49_233500 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A125YP67, triose-phosphate isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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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: 2.26 Å3/Da / Density % sol: 45.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Ammonium Sulphate, 0.1 M Bis-Tris, 25 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97875 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2016 / Details: beryllium lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97875 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 67710 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.04 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.86 / Num. unique all: 3393 / Num. unique obs: 3393 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.721 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.16 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.016 Å2
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Refinement step | Cycle: 1 / Resolution: 2→30 Å
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Refine LS restraints |
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