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Yorodumi- PDB-4jex: Y21K mutant of N-acetylornithine aminotransferase complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jex | ||||||
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Title | Y21K mutant of N-acetylornithine aminotransferase complexed with L-canaline | ||||||
Components | Acetylornithine/succinyldiaminopimelate aminotransferase | ||||||
Keywords | TRANSFERASE / PLP dependent fold type I sub class II aminotransferase | ||||||
Function / homology | Function and homology information succinyldiaminopimelate transaminase / succinyldiaminopimelate transaminase activity / acetylornithine transaminase / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / arginine biosynthetic process / lysine biosynthetic process via diaminopimelate / pyridoxal phosphate binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Bisht, S. / Bharath, S.R. / Murthy, M.R.N. | ||||||
Citation | Journal: To be Published Title: Conformational transitions, ligand specificity and catalysis in N-acetylornithine aminotransferase: Implications on drug designing and rational enzyme engineering in omega aminotransferases Authors: Bisht, S. / Bharath, S.R. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jex.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jex.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 4jex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jex_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4jex_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4jex_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 4jex_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/4jex ftp://data.pdbj.org/pub/pdb/validation_reports/je/4jex | HTTPS FTP |
-Related structure data
Related structure data | 4jeyC 4jezC 4jf0C 4jf1C 2pb0S 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45704.961 Da / Num. of mol.: 2 / Mutation: Y21K, A298T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: argD, dapC, dtu, STM3468 / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta References: UniProt: P40732, acetylornithine transaminase, succinyldiaminopimelate transaminase |
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-Non-polymers , 6 types, 664 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-TNF / | #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: 1.95 Å3/Da / Density % sol: 37.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.5M ammonium acetate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å | |||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2012 / Details: Bent collimating mirror and toroid | |||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.43→112.78 Å / Num. obs: 132710 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PB0 Resolution: 1.43→25.01 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.832 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 11.734 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→25.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.467 Å / Total num. of bins used: 20
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