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Yorodumi- PDB-5dj9: Crystal structure of the ornithine aminotransferase from Toxoplas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dj9 | ||||||
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Title | Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with gabaculine | ||||||
Components | Ornithine aminotransferase, mitochondrial | ||||||
Keywords | TRANSFERASE / inhibitor / complex / parasite / PYRIDOXAL 5'-PHOSPHATE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii ME49 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Flores, K. / Le, H.V. / Silverman, R.B. / McLeod, R.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with gabaculine Authors: Filippova, E.V. / Minasov, G. / Flores, K. / Le, H.V. / Silverman, R.B. / McLeod, R.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dj9.cif.gz | 348.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dj9.ent.gz | 284 KB | Display | PDB format |
PDBx/mmJSON format | 5dj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dj9_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5dj9_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5dj9_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 5dj9_validation.cif.gz | 59.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/5dj9 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/5dj9 | HTTPS FTP |
-Related structure data
Related structure data | 4nogS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48394.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_269110 / Plasmid: pMCSG28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: S8EY38, ornithine aminotransferase |
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-Non-polymers , 5 types, 739 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-BTB / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.12 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350, 5mM gabaculine and 2mM PLP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 109959 / % possible obs: 96.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.2 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NOG Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.061 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 23.099 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→30 Å
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Refine LS restraints |
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