[English] 日本語
Yorodumi- PDB-5lnn: Crystal structure of D1050A mutant of the receiver domain of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lnn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of D1050A mutant of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana | ||||||
Components | Histidine kinase CKI1 | ||||||
Keywords | TRANSFERASE / receiver domain / mutant / histidine kinase CKI1 / (alpha/beta)5 fold | ||||||
Function / homology | Function and homology information secondary growth / embryo sac development / phloem or xylem histogenesis / cytokinin-activated signaling pathway / protein histidine kinase activity / plasmodesma / histidine kinase / phosphorelay sensor kinase activity / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Otrusinova, O. / Demo, G. / Kaderavek, P. / Jansen, S. / Jasenakova, Z. / Pekarova, B. / Janda, L. / Wimmerova, M. / Hejatko, J. / Zidek, L. | ||||||
Funding support | Czech Republic, 1items
| ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana. Authors: Otrusinova, O. / Demo, G. / Padrta, P. / Jasenakova, Z. / Pekarova, B. / Gelova, Z. / Szmitkowska, A. / Kaderavek, P. / Jansen, S. / Zachrdla, M. / Klumpler, T. / Marek, J. / Hritz, J. / ...Authors: Otrusinova, O. / Demo, G. / Padrta, P. / Jasenakova, Z. / Pekarova, B. / Gelova, Z. / Szmitkowska, A. / Kaderavek, P. / Jansen, S. / Zachrdla, M. / Klumpler, T. / Marek, J. / Hritz, J. / Janda, L. / Iwai, H. / Wimmerova, M. / Hejatko, J. / Zidek, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5lnn.cif.gz | 49 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5lnn.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lnn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lnn_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5lnn_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 5lnn_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 5lnn_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/5lnn ftp://data.pdbj.org/pub/pdb/validation_reports/ln/5lnn | HTTPS FTP |
-Related structure data
Related structure data | 5lnmC 5n2nC 3mm4S 5f0t S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23181.869 Da / Num. of mol.: 1 / Fragment: UNP residues 944-1122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CKI1, At2g47430, T30B22.27 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O22267, histidine kinase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
---|---|
Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 5.05 / Details: 2.54 M (NH4)2(SO4), 0.1 M MES pH 5.05 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97522 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97522 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→47.05 Å / Num. obs: 28315 / % possible obs: 98.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 37.9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 5.4 / % possible all: 95.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MM4 Resolution: 1.6→42.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.582 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.084 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.103 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→42.51 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|