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Yorodumi- PDB-2byl: Structure of ornithine aminotransferase triple mutant Y85I Y55A G320F -
+Open data
-Basic information
Entry | Database: PDB / ID: 2byl | ||||||
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Title | Structure of ornithine aminotransferase triple mutant Y85I Y55A G320F | ||||||
Components | ORNITHINE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / DISEASE MUTATION / MITOCHONDRION / TRANSIT PEPTIDE PLP-DEPENDENT ENZYME / POLYMORPHISM / 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 / Resolution: 2.15 Å | ||||||
Authors | Markova, M. / Peneff, C. / Hewlins, M.J.E. / Schirmer, T. / John, R.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Determinants of Substrate Specificity in Omega-Aminotransferases. Authors: Markova, M. / Peneff, C. / Hewlins, M.J.E. / Schirmer, T. / John, R.A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2byl.cif.gz | 249.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2byl.ent.gz | 201.5 KB | Display | PDB format |
PDBx/mmJSON format | 2byl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2byl_validation.pdf.gz | 402.3 KB | Display | wwPDB validaton report |
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Full document | 2byl_full_validation.pdf.gz | 411.6 KB | Display | |
Data in XML | 2byl_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 2byl_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/2byl ftp://data.pdbj.org/pub/pdb/validation_reports/by/2byl | HTTPS FTP |
-Related structure data
Related structure data | 2byjC 1oatS S: Starting model for refinement C: citing same article (ref.) |
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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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 48541.676 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 / References: UniProt: P04181, ornithine aminotransferase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 85 TO ILE ENGINEERED RESIDUE IN CHAIN A, TYR 55 TO ALA ...ENGINEERED | |
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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: 7.9 Details: 6-10%PEG6000, 120-160MM NACL, 50MM TRICINE PH7.9, 1MM DTT, pH 7.90 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.977 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 26, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.22 Å / Num. obs: 78515 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 5.86 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 5.17 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.41 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OAT Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.915 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.155 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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