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Yorodumi- PDB-3ei9: Crystal structure of K270N variant of LL-diaminopimelate aminotra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ei9 | ||||||
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Title | Crystal structure of K270N variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with L-Glu: External aldimine form | ||||||
Components | LL-diaminopimelate aminotransferase | ||||||
Keywords | TRANSFERASE / aminotransferase / lysine biosynthesis / Pyridoxal 5' phosphate / external aldimine / LL-diaminopimelate / Chloroplast / Pyridoxal phosphate / Transit peptide | ||||||
Function / homology | Function and homology information LL-diaminopimelate aminotransferase / L,L-diaminopimelate aminotransferase activity / systemic acquired resistance, salicylic acid mediated signaling pathway / transaminase activity / lysine biosynthetic process via diaminopimelate / chloroplast stroma / chloroplast / pyridoxal phosphate binding / copper ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Watanabe, N. / Clay, M.D. / van Belkum, M.J. / Cherney, M.M. / Vederas, J.C. / James, M.N.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana. Authors: Watanabe, N. / Clay, M.D. / van Belkum, M.J. / Cherney, M.M. / Vederas, J.C. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ei9.cif.gz | 196.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ei9.ent.gz | 153.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ei9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ei9_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3ei9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3ei9_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 3ei9_validation.cif.gz | 65.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/3ei9 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/3ei9 | HTTPS FTP |
-Related structure data
Related structure data | 3ei5C 3ei6C 3ei7C 3ei8C 3eiaC 3eibC 2z20S C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 47502.570 Da / Num. of mol.: 2 / Fragment: UNP residues 36 to 461 / Mutation: K270N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DAP, AGD2, At4g33680, T16L1.170 / Production host: Escherichia coli (E. coli) References: UniProt: Q93ZN9, LL-diaminopimelate aminotransferase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: 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: 2.74 Å3/Da / Density % sol: 55.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 45% (NH4)2SO4, 0.1 M HEPES pH 7.5, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2007 |
Radiation | Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115872 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. all: 151099 / Num. obs: 151099 / % possible obs: 99.9 % / Rsym value: 0.082 |
Reflection shell | Resolution: 1.55→1.61 Å / Rsym value: 0.443 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2Z20 Resolution: 1.55→39.44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.067 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / 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: 19.451 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→39.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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