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- PDB-1lyx: Plasmodium Falciparum Triosephosphate Isomerase (PfTIM)-Phosphogl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lyx | ||||||
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Title | Plasmodium Falciparum Triosephosphate Isomerase (PfTIM)-Phosphoglycolate complex | ||||||
![]() | Triosephosphate Isomerase | ||||||
![]() | ISOMERASE / TIM barrels / beta-alpha barrels | ||||||
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 | ![]() ![]() | ||||||
![]() | Parthasarathy, S. / Balaram, H. / Balaram, P. / Murthy, M.R. | ||||||
![]() | ![]() Title: Structure of the Plasmodium falciparum triosephosphate isomerase-phosphoglycolate complex in two crystal forms: characterization of catalytic loop open and closed conformations in the ligand-bound state Authors: Parthasarathy, S. / Ravindra, G. / Balaram, H. / Balaram, P. / Murthy, M.R. #1: ![]() Title: Triosephosphate isomerase from Plasmodium falciparum: Crystal structure provides insights into antimalarial drug design Authors: Velankar, S.S. / Ray, S.S. / Gokhle, R.S. / Suma, S. / Balaram, H. / Balaram, P. / Murthy, M.R.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.1 KB | Display | ![]() |
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PDB format | ![]() | 48.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 456.2 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lzoC ![]() 1ydvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27997.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TPI / Plasmid: ptrc 99A vector, called pARC / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-PGA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 46.74 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% to 25% PEG 6000 or PEG 4000 or PEG 3350 or PEG 1450 in the presence of EDTA, DTT and Sodium azide in 100mM MES. pH 6.5, VAPOR DIFFUSION, HANGING DROP at 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2000 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 20508 / Num. obs: 20508 / % possible obs: 98.4 % / Redundancy: 18.8 % / Rsym value: 0.068 |
Reflection shell | Resolution: 1.9→1.97 Å / Num. unique all: 2008 / Rsym value: 0.215 / % possible all: 97.1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 10508 / Num. measured all: 198026 / Rmerge(I) obs: 0.068 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Monomer of unbound PfTIM, PDB code 1YDV Resolution: 1.9→20 Å / Data cutoff high absF: 416213.98 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: Engh & Huber Details: Bulk solvent and anisotropic B-scaling were applied throughout the refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.54 Å2 / ksol: 0.355873 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.74 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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