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- PDB-3mm4: Crystal structure of the receiver domain of the histidine kinase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mm4 | ||||||
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Title | Crystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana | ||||||
![]() | Histidine kinase homolog | ||||||
![]() | TRANSFERASE / receiver domain / CKI1 / Arabidopsis / cytokinin signaling / Rossmann-fold / CheY-like | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Marek, J. / Klumpler, T. / Pekarova, B. / Triskova, O. / Horak, J. / Zidek, L. / Dopitova, R. / Hejatko, J. / Janda, L. | ||||||
![]() | ![]() Title: Structure and binding specificity of the receiver domain of sensor histidine kinase CKI1 from Arabidopsis thaliana. Authors: Pekarova, B. / Klumpler, T. / Triskova, O. / Horak, J. / Jansen, S. / Dopitova, R. / Borkovcova, P. / Papouskova, V. / Nejedla, E. / Sklenar, V. / Marek, J. / Zidek, L. / Hejatko, J. / Janda, L. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Cloning, purification, crystallization and preliminary X-ray analysis of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana. Authors: Klumpler, T. / Pekarova, B. / Marek, J. / Borkovcova, P. / Janda, L. / Hejatko, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47 KB | Display | ![]() |
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PDB format | ![]() | 32.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 433.7 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mmnC ![]() 1ab5S 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: 23225.879 Da / Num. of mol.: 1 / Fragment: Receiver Domain (UNP Residues 944-1122) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.05 Details: 0.1M MES, 2.54M Ammonium sulfate, pH 5.05, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 2→5 Å / Num. all: 15054 / Num. obs: 13674 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2→2.043 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.296 / % possible all: 75.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AB5 (CheY) Resolution: 2→5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.44 / SU B: 3.106 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.605 Å2
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Refinement step | Cycle: LAST / Resolution: 2→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.043 Å / Total num. of bins used: 20
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