+Open data
-Basic information
Entry | Database: PDB / ID: 1oat | ||||||
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Title | ORNITHINE AMINOTRANSFERASE | ||||||
Components | ORNITHINE AMINOTRANSFERASE | ||||||
Keywords | AMINOTRANSFERASE / PLP-DEPENDENT ENZYME / PYRIDOXAL PHOSPHATE | ||||||
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 / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, NON-CRYSTALLOGRAPHIC AVERAGING / Resolution: 2.5 Å | ||||||
Authors | Shen, B.W. / Schirmer, T. / Jansonius, J.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of human recombinant ornithine aminotransferase. Authors: Shen, B.W. / Hennig, M. / Hohenester, E. / Jansonius, J.N. / Schirmer, T. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Recombinant Human Ornithine Aminotransferase Authors: Shen, B.W. / Ramesh, V. / Mueller, R. / Hohenester, E. / Hennig, M. / Jansonius, J.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oat.cif.gz | 245.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oat.ent.gz | 202 KB | Display | PDB format |
PDBx/mmJSON format | 1oat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oat_validation.pdf.gz | 462.7 KB | Display | wwPDB validaton report |
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Full document | 1oat_full_validation.pdf.gz | 485.6 KB | Display | |
Data in XML | 1oat_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 1oat_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/1oat ftp://data.pdbj.org/pub/pdb/validation_reports/oa/1oat | HTTPS FTP |
-Related structure data
Related structure data | 1dgdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 48593.668 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Plasmid: PASK40 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83 / References: UniProt: P04181, ornithine aminotransferase #2: Chemical | #3: 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: 2.78 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 / Details: pH 7.8 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 51.9 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Oct 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 52220 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.082 |
Reflection shell | Redundancy: 5.6 % / Rmerge(I) obs: 0.35 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 38 Å |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.349 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, NON-CRYSTALLOGRAPHIC AVERAGING Starting model: DIALKYLGLYCINE DECARBOXYLASE, PDB ENTRY 1DGD Resolution: 2.5→38 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 19.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.53 Å / Total num. of bins used: 30
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.171 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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