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Yorodumi- PDB-4jew: N-acetylornithine aminotransferase from S. typhimurium complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jew | ||||||
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Title | N-acetylornithine aminotransferase from S. typhimurium 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: 1.48 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 | 4jew.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jew.ent.gz | 141.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jew_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4jew_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4jew_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 4jew_validation.cif.gz | 55.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/4jew ftp://data.pdbj.org/pub/pdb/validation_reports/je/4jew | HTTPS FTP |
-Related structure data
Related structure data | 4jevC 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: 45738.957 Da / Num. of mol.: 2 / Mutation: 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 , 5 types, 697 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-TNF / | #6: 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: 36.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 20% PEG 3350, 0.5M ammonium acetate, 0.1M CAPSO pH 9.5, 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: 1.48→112.33 Å / Num. obs: 119395 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.5 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PB0 Resolution: 1.48→28.08 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.902 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.064 / 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: 10.489 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→28.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.479→1.517 Å / Total num. of bins used: 20
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