[English] 日本語
Yorodumi- PDB-4pac: Crystal Structure of Histidine-containing Phosphotransfer Protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pac | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Histidine-containing Phosphotransfer Protein AHP2 from Arabidopsis thaliana | |||||||||||||||||||||
Components | Histidine-containing phosphotransfer protein 2 | |||||||||||||||||||||
Keywords | SIGNALING PROTEIN / cytokinin signaling / helical fold | |||||||||||||||||||||
Function / homology | Function and homology information antipodal cell differentiation / embryo sac egg cell differentiation / protein histidine kinase binding / cytokinin-activated signaling pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / phosphorylation / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.53 Å | |||||||||||||||||||||
Authors | Degtjarik, O. / Dopitova, R. / Puehringer, S. / Weiss, M.S. / Janda, L. / Hejatko, J. / Kuta-Smatanova, I. | |||||||||||||||||||||
Funding support | Czech Republic, 6items
| |||||||||||||||||||||
Citation | Journal: To Be Published Title: Crystal structure of AHP2 from Arabidopsis thaliana Authors: Degtjarik, O. / Dopitova, R. / Puehringer, S. / Reha, D. / Otrusinova, O. / Pekarova, B. / Kuty, M. / Zidek, L. / Janda, L. / Weiss, M.S. / Kuta-Smatanova, I. / Hejatko, H. | |||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pac.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pac.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 4pac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/4pac ftp://data.pdbj.org/pub/pdb/validation_reports/pa/4pac | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22369.232 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHP2, ATHP1, At3g29350, MUO10.6 / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q9ZNV8 |
---|---|
#2: Chemical | ChemComp-MES / |
#3: Chemical | ChemComp-IMD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.84 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1M MES, 1.6M magnesium sulfate / PH range: 5.8 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→50 Å / Num. obs: 10808 / % possible obs: 99.6 % / Redundancy: 7 % / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.53→2.68 Å / % possible obs: 98.7 % / Redundancy: 7.02 % / Rmerge(I) obs: 1.014 / Mean I/σ(I) obs: 1.76 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 2.53→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.856 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 59.628 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.53→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|