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- PDB-1m7p: Plasmodium Falciparum Triosephosphate isomerase (PfTIM) compled t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m7p | ||||||
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Title | Plasmodium Falciparum Triosephosphate isomerase (PfTIM) compled to substrate analog glycerol-3-phosphate (G3P). | ||||||
![]() | Triosephosphate Isomerase | ||||||
![]() | ISOMERASE / TIM barrles / beta-alpha barrels / enzyme-inhibitor complex | ||||||
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.N. | ||||||
![]() | ![]() Title: Structures of Plasmodium falciparum triosephosphate isomerase complexed to substrate analogues: observation of the catalytic loop in the open conformation in the ligand-bound state. Authors: Parthasarathy, S. / Balaram, H. / Balaram, P. / Murthy, M.R. #1: ![]() Title: Triosephosphate Isomerase From Plasmodium Falciparum: Crystal Structure Proveides Insights into Antimalarial Drug Design. Authors: Velankar, S.S. / Ray, S.S. / Gokle, 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 | ![]() | 110.4 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.2 KB | Display | ![]() |
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Full document | ![]() | 462.6 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m7oC ![]() 1ydvS S: Starting model for refinement C: citing same article ( |
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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.) ![]() ![]() Gene: TPI / Plasmid: ptrc 99A vector, called pARC / Production host: ![]() ![]() #2: Chemical | #3: 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: 43.5 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 12% to 20% PEG 1450 in 100mm Sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||
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: Jun 11, 1999 / 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: 2.4→20 Å / Num. obs: 19337 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.115 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1824 / Rsym value: 0.356 / % possible all: 96.4 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. measured all: 98166 / Rmerge(I) obs: 0.115 |
Reflection shell | *PLUS % possible obs: 96.4 % / Rmerge(I) obs: 0.356 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Dimer of Unbound PfTIM; PDB code 1YDV Resolution: 2.4→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 156570.02 / Data cutoff high rms absF: 156570.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: Engh & Huber Details: Maximum Likelihood in Amplitutes (AMLF) protocol used. Anisotropic B-scaling, Bluk solvent correction and 2-fold NCS restraints were used throughout the refinement.
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Solvent computation | Bsol: 30.5807 Å2 / ksol: 0.335689 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å / Rfactor Rfree: 0.219 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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