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Open data
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Basic information
Entry | Database: PDB / ID: 1ydv | ||||||
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Title | TRIOSEPHOSPHATE ISOMERASE (TIM) | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE | ||||||
![]() | ISOMERASE / GLYCOLYSIS / GLUCONEOGENESIS | ||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Velankar, S.S. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Triosephosphate isomerase from Plasmodium falciparum: the crystal structure provides insights into antimalarial drug design. Authors: Velanker, S.S. / Ray, S.S. / Gokhale, R.S. / Suma, S. / Balaram, H. / Balaram, P. / Murthy, M.R. #1: ![]() Title: Cloning of the Triosephosphate Isomerase Gene of Plasmodium Falciparum and Expression in Escherichia Coli Authors: Ranie, J. / Kumar, V.P. / Balaram, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.7 KB | Display | ![]() |
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PDB format | ![]() | 85 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.8 KB | Display | ![]() |
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Full document | ![]() | 418.7 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27997.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 48.01 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 10 MG/ML PROTEIN IN 12% PEG 6000 IN HEPES BUFFER PH 7.5, 1MM DTT EQUILIBRATED AGAINST 24% PEG 6000 IN HEPES BUFFER PH 7.5, 1MM DTT | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: FRANCS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 25936 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.089 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.252 / % possible all: 83.9 |
Reflection | *PLUS Num. measured all: 39357 |
Reflection shell | *PLUS % possible obs: 83.9 % / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: TRYPANOSOMAL TIM Resolution: 2.2→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: LYS A 12 AND LYS B 12 HAVE POSITIVE PHI ANGLE WHICH IS IMPORTANT FOR THE ACTIVITY OF THE PROTEIN.
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Displacement parameters | Biso mean: 14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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