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- PDB-8j7c: Crystal structure of triosephosphate isomerase from Leishmania or... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8j7c | |||||||||
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Title | Crystal structure of triosephosphate isomerase from Leishmania orientalis at 1.88A with an arsenic ion bound at Cys57 | |||||||||
![]() | Triosephosphate isomerase | |||||||||
![]() | ISOMERASE / triosephosphate isomerase / TIM-barrel / dimer / an arsenic atom bound at Cys57 | |||||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kuaprasert, B. / Attarataya, J. / Riangrungroj, P. / Pornthanakasem, W. / Suginta, W. / Mungthin, M. / Leelayoova, S. / Choowongkomon, K. / Leartsakulpanich, U. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Leishmania orientalis triosephosphate isomerase crystal structure at 1.45 angstroms resolution and its potential specific inhibitors Authors: Kuaprasert, B. / Leartsakulpanich, U. / Riangrungroj, P. / Pornthanakasem, W. / Suginta, W. / Robinson, R. / Zhou, Y. / Mungthin, M. / Leelayoova, S. / Saehlee, S. / Kiriwan, D. / Choowongkomon, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.7 KB | Display | ![]() |
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PDB format | ![]() | 88.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
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Full document | ![]() | 444.1 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jbpC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 29244.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): lstim gene was ligated into pET15b at NdeI and BamHI sites Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.12 % / Description: rod shape |
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Crystal grow | Temperature: 291.15 K / Method: microbatch / pH: 5.9 Details: Equal volumes (1.0 microliter) of enzyme (24.2 mg/ml in 50 mM potassium phosphate buffer, pH 8.0, containing 50 mM KCl, 5 mM DTT, and 10% glycerol) and precipitant (PEG8000 18% w/v in 0.2 mM ...Details: Equal volumes (1.0 microliter) of enzyme (24.2 mg/ml in 50 mM potassium phosphate buffer, pH 8.0, containing 50 mM KCl, 5 mM DTT, and 10% glycerol) and precipitant (PEG8000 18% w/v in 0.2 mM calcium acetate hydrate, 0.1 M and sodium cacodylate trihydrate, pH 5.9) PH range: 5.9 - 6.5 / Temp details: Incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 700 series Oxford Cryosystems / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2015 / Details: spherical mirror for CM and toroidal mirror for M |
Radiation | Monochromator: SI(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.55 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→21.56 Å / Num. obs: 46160 / % possible obs: 98.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 6.92 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.059 / Rrim(I) all: 0.101 / Net I/av σ(I): 7.2 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.88→1.92 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2463 / CC1/2: 0.598 / Rpim(I) all: 0.399 / Rrim(I) all: 0.682 / % possible all: 81.2 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.047 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→19.98 Å
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Refine LS restraints |
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