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- PDB-3ei5: Crystal structure of LL-diaminopimelate aminotransferase from Ara... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ei5 | ||||||
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Title | Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with PLP-Glu: an external aldimine mimic | ||||||
![]() | LL-diaminopimelate aminotransferase | ||||||
![]() | TRANSFERASE / aminotransferase / lysine biosynthesis / Pyridoxal 5' phosphate / external aldimine / LL-diaminopimelate / Chloroplast / Pyridoxal phosphate / Transit peptide | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watanabe, N. / Clay, M.D. / van Belkum, M.J. / Cherney, M.M. / Vederas, J.C. / James, M.N.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.3 KB | Display | ![]() |
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PDB format | ![]() | 141.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 52.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ei6C ![]() 3ei7C ![]() 3ei8C ![]() 3ei9C ![]() 3eiaC ![]() 3eibC ![]() 2z20S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47517.648 Da / Num. of mol.: 2 / Fragment: UNP residues 36 to 461 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.22 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2007 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978483 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→40 Å / Num. all: 62726 / Num. obs: 62726 / % possible obs: 94.5 % / Rsym value: 0.116 |
Reflection shell | Resolution: 2.05→2.12 Å / Rsym value: 0.586 / % possible all: 68.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2Z20 Resolution: 2.05→39.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.065 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.16 / 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: 29.898 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→39.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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