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- PDB-5upr: X-ray structure of a putative triosephosphate isomerase from Toxo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5upr | ||||||
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Title | X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49 | ||||||
![]() | Triosephosphate isomerase | ||||||
![]() | ISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 414.4 KB | Display | ![]() |
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PDB format | ![]() | 354 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.5 KB | Display | ![]() |
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Full document | ![]() | 460.9 KB | Display | |
Data in XML | ![]() | 48.2 KB | Display | |
Data in CIF | ![]() | 72 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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.) ![]() ![]() Strain: ATCC 50611 / Me49 / Gene: TPI-II, TGME49_233500 / Plasmid: pMCSG7 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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