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Yorodumi- PDB-4zlv: Crystal structure of the ornithine aminotransferase from Toxoplas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zlv | ||||||
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Title | Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with the Schiff base between PLP and Lys286 | ||||||
Components | Ornithine aminotransferase, mitochondrial, putative | ||||||
Keywords | TRANSFERASE / Structural Genomics / pyridoxal 5'-phosphate (PLP)-independent aminotransferase / 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: 1.8 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Flores, K. / Van Le, H. / Silverman, R.B. / McLeod, R. / 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 the Schiff base between PLP and Lys286 Authors: Filippova, E.V. / Minasov, G. / Flores, K. / Van Le, H. / Silverman, R.B. / McLeod, R. / 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 | 4zlv.cif.gz | 346.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zlv.ent.gz | 284.3 KB | Display | PDB format |
PDBx/mmJSON format | 4zlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zlv_validation.pdf.gz | 468.1 KB | Display | wwPDB validaton report |
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Full document | 4zlv_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 4zlv_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 4zlv_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/4zlv ftp://data.pdbj.org/pub/pdb/validation_reports/zl/4zlv | HTTPS FTP |
-Related structure data
Related structure data | 4ngoS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 19 - 439 / Label seq-ID: 19 - 439
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-Components
#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)/pMagic / References: UniProt: S8EY38, ornithine aminotransferase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PEG / | #5: 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: 2.11 Å3/Da / Density % sol: 41.76 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97889 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97889 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 70729 / Num. obs: 70729 / % possible obs: 96 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5 / % possible all: 87.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NGO Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.978 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.124 / 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: 35.798 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→30 Å
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