[English] 日本語
Yorodumi- PDB-3ei6: Crystal structure of LL-diaminopimelate aminotransferase from Ara... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ei6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with PLP-DAP: an external aldimine mimic | ||||||
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: 1.9 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ei6.cif.gz | 186.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ei6.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ei6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ei6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ei6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3ei6_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 3ei6_validation.cif.gz | 57.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/3ei6 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/3ei6 | HTTPS FTP |
-Related structure data
Related structure data | 3ei5C 3ei7C 3ei8C 3ei9C 3eiaC 3eibC 2z20S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) 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 | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.37 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 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: 1.9→40 Å / Num. all: 78472 / Num. obs: 78472 / % possible obs: 94.1 % / Rsym value: 0.053 |
Reflection shell | Resolution: 1.9→1.97 Å / Rsym value: 0.256 / % possible all: 66.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2Z20 Resolution: 1.9→39.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.32 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 24.995 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.899→1.948 Å / Total num. of bins used: 20
|