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- PDB-2oma: Crystallographic analysis of a chemically modified triosephosphat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oma | ||||||
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Title | Crystallographic analysis of a chemically modified triosephosphate isomerase from Trypanosoma cruzi with dithiobenzylamine (DTBA) | ||||||
![]() | Triosephosphate isomerase | ||||||
![]() | ISOMERASE / Triosephosphate isomerase / Trypanosoma cruzi / protein interfaces / dithiobisbenzylamine | ||||||
Function / homology | ![]() glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rodriguez-Romero, A. / Gomez-Puyou, A. | ||||||
![]() | ![]() Title: Perturbation of the Dimer Interface of Triosephosphate Isomerase and its Effect on Trypanosoma cruzi. Authors: Olivares-Illana, V. / Rodriguez-Romero, A. / Becker, I. / Berzunza, M. / Garcia, J. / Perez-Montfort, R. / Cabrera, N. / Lopez-Calahorra, F. / de Gomez-Puyou, M.T. / Gomez-Puyou, A. #1: ![]() Title: Inactivation of triosephosphate isomerase from trypanosoma cruzi by an agent AN AGENT THAT PERTURBS ITS DIMER INTERFACE. Authors: Tellez-Valencia, A. / Olivares-Illana, V. / Hernandez-Santoyo, A. / Perez-Montfort, R. / Costas, M. / Rodriguez-Romero, A. / Lopez-Calahorra, F. / Tuena de Gomez-Puyou, M. / Gomez-Puyou, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.2 KB | Display | ![]() |
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PDB format | ![]() | 89.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1tcdS 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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Unit cell |
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Details | The biological assembly is a dimer |
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Components
#1: Protein | Mass: 27352.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 5 MICROL OF THE PROTEIN SOLUTION WERE MIXED WITH 5 MICROL OF 2 % POLYETHYLENE GLYCOL 400, 0.1 M HEPES, 2.0M AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, PH 7.50. ...Details: 5 MICROL OF THE PROTEIN SOLUTION WERE MIXED WITH 5 MICROL OF 2 % POLYETHYLENE GLYCOL 400, 0.1 M HEPES, 2.0M AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, PH 7.50. CRYSTAL SOAKED IN DITHIOBENZYLAMINE |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 3, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→41.45 Å / Num. obs: 23141 / % possible obs: 91 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.8 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TCD Resolution: 2.15→41.45 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.324 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOMS ARE ASSIGNED REDUCED OCCUPANCIES WHEN ELECTRON DENSITY IS WEAK OR ATOMS HAVE PARTIAL OCCUPANCY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.788 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→41.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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