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Yorodumi- PDB-4nog: Crystal structure of a putative ornithine aminotransferase from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nog | ||||||
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Title | Crystal structure of a putative ornithine aminotransferase from Toxoplasma gondii ME49 in complex with pyrodoxal-5'-phosphate | ||||||
Components | Putative ornithine aminotransferase, mitochondrial | ||||||
Keywords | TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / ornithine aminotransferase / Toxoplasma | ||||||
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 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Filippova, E.V. / Halavaty, A. / Ruan, J. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Ngo, H. / Shanmugam, D. / Roos, D. / Anderson, W.F. ...Filippova, E.V. / Halavaty, A. / Ruan, J. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Ngo, H. / Shanmugam, D. / Roos, D. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Front Cell Infect Microbiol / Year: 2018 Title: CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii . Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. ...Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. / Moulton, J.D. / Moulton, H. / McPhillie, M.J. / Muench, S.P. / Fishwick, C.W.G. / Sabini, E. / Shanmugam, D. / Roos, D.S. / McLeod, R. / Anderson, W.F. / Ngo, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nog.cif.gz | 381.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nog.ent.gz | 309.6 KB | Display | PDB format |
PDBx/mmJSON format | 4nog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nog_validation.pdf.gz | 501.5 KB | Display | wwPDB validaton report |
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Full document | 4nog_full_validation.pdf.gz | 510.7 KB | Display | |
Data in XML | 4nog_validation.xml.gz | 42.9 KB | Display | |
Data in CIF | 4nog_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/4nog ftp://data.pdbj.org/pub/pdb/validation_reports/no/4nog | HTTPS FTP |
-Related structure data
Related structure data | 4nmlC 4nu7C 4o0nC 4odiC 5bxiC 3lg0S S: Starting model for refinement C: citing same article (ref.) |
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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: 49027.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGME49_069110, TGME49_269110 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: S8EY38, ornithine aminotransferase |
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-Non-polymers , 6 types, 1048 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-BTB / | #6: Chemical | ChemComp-PEG / | #7: 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: 2.08 Å3/Da / Density % sol: 40.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium Acetate, 0.1 M Bis-Tris, 35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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: Oct 31, 2013 / Details: beryllium lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→62.14 Å / Num. all: 224574 / Num. obs: 224574 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / Num. unique all: 11241 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LG0 Resolution: 1.2→62.14 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.639 / SU ML: 0.032 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.04 / 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: 18.365 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→62.14 Å
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Refine LS restraints |
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