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Yorodumi- PDB-4y31: Crystal structure of yellow lupine LlPR-10.1A protein in ligand-f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y31 | ||||||
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Title | Crystal structure of yellow lupine LlPR-10.1A protein in ligand-free form | ||||||
Components | Protein LlR18A | ||||||
Keywords | PLANT PROTEIN / PR-10 FOLD / LIGAND BINDING / PHYTOHORMONE BINDING PROTEIN / TRANS-ZEATIN / CYTOKININ | ||||||
Function / homology | Function and homology information 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 / cytosol Similarity search - Function | ||||||
Biological species | Lupinus luteus (yellow lupine) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Sliwiak, J. / Michalska, K. / Sikorski, M.M. / Jaskolski, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y31.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y31.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 4y31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/4y31 ftp://data.pdbj.org/pub/pdb/validation_reports/y3/4y31 | HTTPS FTP |
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-Related structure data
Related structure data | 4ryvC 5c9yC 1icxS 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
#1: Protein | Mass: 16748.924 Da / Num. of mol.: 1 / Fragment: UNP residues 2-156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lupinus luteus (yellow lupine) / Gene: LLR18A / Plasmid: PET-3A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52778 |
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#2: Chemical | ChemComp-ACT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 18% PEG4000, 0.2 M sodium acetate, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→30 Å / Num. obs: 29618 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.32→1.37 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1icx Resolution: 1.32→28.27 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.363 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.063 / 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: 19.97 Å2
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Refinement step | Cycle: 1 / Resolution: 1.32→28.27 Å
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Refine LS restraints |
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