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- PDB-4ryv: Crystal structure of yellow lupin LLPR-10.1A protein in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ryv | ||||||
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Title | Crystal structure of yellow lupin LLPR-10.1A protein in complex with trans-zeatin | ||||||
![]() | Protein LLPR-10.1A | ||||||
![]() | PLANT PROTEIN / PR-10 FOLD / LIGAND BINDING / PHYTOHORMONE BINDING PROTEIN / TRANS-ZEATIN / CYTOKININ | ||||||
Function / homology | ![]() cytokinin binding / response to biotic stimulus / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity ...cytokinin binding / response to biotic stimulus / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dolot, R. / Michalska, K. / Sliwiak, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M. | ||||||
![]() | ![]() Title: Crystallographic and CD probing of ligand-induced conformational changes in a plant PR-10 protein. Authors: Sliwiak, J. / Dolot, R. / Michalska, K. / Szpotkowski, K. / Bujacz, G. / Sikorski, M. / Jaskolski, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.7 KB | Display | ![]() |
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PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 448 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y31C ![]() 5c9yC ![]() 1icxS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 16748.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-ZEA / ( #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.37 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 M (NH4)2SO4, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 29, 2005 |
Radiation | Monochromator: SINGLE ASYMMETRICALLY CUT SI(111) CRYSTAL WITH HORIZONTAL DIFFRACTION PLANE Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0605 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→99 Å / Num. obs: 34754 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.74 |
Reflection shell | Resolution: 1.38→1.43 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 6.48 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ICX Resolution: 1.38→42.49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.961 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.051 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.105 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→42.49 Å
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Refine LS restraints |
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