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Yorodumi- PDB-2dtj: Crystal structure of regulatory subunit of aspartate kinase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dtj | ||||||
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Title | Crystal structure of regulatory subunit of aspartate kinase from Corynebacterium glutamicum | ||||||
Components | Aspartokinase | ||||||
Keywords | TRANSFERASE / protein-ligand complex / regulatory subunit | ||||||
Function / homology | Function and homology information aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Yoshida, A. / Tomita, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural Insight into Concerted Inhibition of alpha(2)beta(2)-Type Aspartate Kinase from Corynebacterium glutamicum Authors: Yoshida, A. / Tomita, T. / Kurihara, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M. #1: Journal: APPL.MICROBIOL.BIOTECHNOL. / Year: 1990 Title: Cloning of a DNA fragment from Corynebacterium glutamicum conferring aminoethyl cysteine resistance and feedback resistance to aspartokinase Authors: Thierbach, G. / Kalinowski, J. / Bachmann, B. / Puhler, A. #2: Journal: MOL.MICROBIOL. / Year: 1991 Title: Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum Authors: Kalinowski, J. / Cremer, J. / Bachmann, B. / Eggeling, L. / Sahm, H. / Puhler, A. #3: Journal: Biochem.Biophys.Res.Commun. / Year: 2004 Title: Conversion of feedback regulation in aspartate kinase by domain exchange Authors: Kato, C. / Kurihara, T. / Kobashi, N. / Yamane, H. / Nishiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dtj.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dtj.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 2dtj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dtj_validation.pdf.gz | 476.9 KB | Display | wwPDB validaton report |
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Full document | 2dtj_full_validation.pdf.gz | 481.9 KB | Display | |
Data in XML | 2dtj_validation.xml.gz | 18 KB | Display | |
Data in CIF | 2dtj_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/2dtj ftp://data.pdbj.org/pub/pdb/validation_reports/dt/2dtj | HTTPS FTP |
-Related structure data
Related structure data | 2dt9S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19384.752 Da / Num. of mol.: 2 Fragment: regulatory subunit, Aspartokinase alpha subunit and Aspartokinase beta subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Plasmid: PET26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus RIL / References: UniProt: P26512, aspartate kinase #2: Chemical | #3: Chemical | ChemComp-CIT / | #4: 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: 2.07 Å3/Da / Density % sol: 40.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M Ammonium Sulfate, 0.1M Citrate, 36 %(w/v) PEG 4000, 10mM threonine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 28, 2006 / Details: mirror |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. all: 43305 / Num. obs: 43305 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.58→1.64 Å / Mean I/σ(I) obs: 3.5 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DT9 Resolution: 1.58→35.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1384008.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.8861 Å2 / ksol: 0.37687 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.58→35.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.68 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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