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- PDB-5lnn: Crystal structure of D1050A mutant of the receiver domain of the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lnn | ||||||
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Title | Crystal structure of D1050A mutant of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana | ||||||
![]() | Histidine kinase CKI1 | ||||||
![]() | TRANSFERASE / receiver domain / mutant / histidine kinase CKI1 / (alpha/beta)5 fold | ||||||
Function / homology | ![]() 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 / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Otrusinova, O. / Demo, G. / Kaderavek, P. / Jansen, S. / Jasenakova, Z. / Pekarova, B. / Janda, L. / Wimmerova, M. / Hejatko, J. / Zidek, L. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49 KB | Display | ![]() |
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PDB format | ![]() | 32.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 435 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lnmC ![]() 5n2nC ![]() 3mm4S ![]() 5f0t S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() Production host: ![]() ![]() References: UniProt: O22267, histidine kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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: 32.103 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→42.51 Å
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Refine LS restraints |
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