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Yorodumi- PDB-5n2n: Crystal structure of the receiver domain of the histidine kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n2n | ||||||
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Title | Crystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana complexed with Mg2+ and BeF3- | ||||||
Components | Histidine kinase CKI1 | ||||||
Keywords | TRANSFERASE / receiver domain / 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: 2.05 Å | ||||||
Authors | Otrusinova, O. / Demo, G. / Padrta, P. / Jasenakova, Z. / Pekarova, B. / Gelova, Z. / Szmitkowska, A. / Kaderavek, P. / Jansen, S. / Zachrdla, M. ...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. | ||||||
Funding support | Czech Republic, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n2n.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n2n.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 5n2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/5n2n ftp://data.pdbj.org/pub/pdb/validation_reports/n2/5n2n | HTTPS FTP |
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-Related structure data
Related structure data | 5lnmC 5lnnC 3mm4S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23225.879 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-BEF / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.27 % / Description: prism |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.05 Details: 2.54 M (NH4)2(SO4), 0.1 M MES pH 5.05, 12% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→46.74 Å / Num. obs: 13705 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.1 / CC1/2: 0.945 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MM4 Resolution: 2.05→42.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.034 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.22 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→42.47 Å
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