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Yorodumi- PDB-2zho: Crystal structure of the regulatory subunit of aspartate kinase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zho | ||||||
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Title | Crystal structure of the regulatory subunit of aspartate kinase from Thermus thermophilus (ligand free form) | ||||||
Components | Aspartokinase | ||||||
Keywords | TRANSFERASE / regulatory domain / ACT domain / Alternative initiation / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Kinase / Lysine biosynthesis | ||||||
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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Yoshida, A. / Tomita, T. / Kuzuyama, T. / Nishiyama, M. | ||||||
Citation | Journal: Febs J. / Year: 2009 Title: Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus Authors: Yoshida, A. / Tomita, T. / Kono, H. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M. #1: Journal: J.Biosci.Bioeng. / Year: 1999 Title: Kinetic and mutation analyses of aspartate kinase from Thermus flavus Authors: Kobashi, N. / Nishiyama, M. / Tanokura, M. #2: Journal: Microbiology / Year: 1995 Title: An operon encoding aspartokinase and purine phosphoribosyltransferase in Thermus flavus Authors: Nishiyama, M. / Kukimoto, M. / Beppu, T. / Horinouchi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zho.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zho.ent.gz | 136.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zho_validation.pdf.gz | 479.2 KB | Display | wwPDB validaton report |
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Full document | 2zho_full_validation.pdf.gz | 505 KB | Display | |
Data in XML | 2zho_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 2zho_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/2zho ftp://data.pdbj.org/pub/pdb/validation_reports/zh/2zho | HTTPS FTP |
-Related structure data
Related structure data | 2dt9SC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 17738.367 Da / Num. of mol.: 6 Fragment: regulatory subunit, Aspartokinase subunit alpha and beta, UNP residues 245-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: AT-62 / Gene: ask / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P61489, aspartate kinase #2: 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: 2.72 Å3/Da / Density % sol: 54.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.6M sodium chloride, 0.1M Sodium citrate, 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: Jun 1, 2006 / Details: mirror |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→46.41 Å / Num. all: 22878 / Num. obs: 22878 / % possible obs: 99.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 67.7 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.98→3.09 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.23 / Rsym value: 0.371 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DT9 Resolution: 2.98→46.41 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2406887.39 / 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: 36.2789 Å2 / ksol: 0.309011 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.98→46.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.98→3.17 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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