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Yorodumi- PDB-5c9y: Crystal structure of yellow lupine LlPR-10.1A protein partially s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c9y | ||||||
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Title | Crystal structure of yellow lupine LlPR-10.1A protein partially saturated with trans-zeatin | ||||||
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 / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Lupinus luteus (yellow lupine) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Sliwiak, J. / Sikorski, M.M. / Jaskolski, M. | ||||||
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 | 5c9y.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c9y.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 5c9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c9y_validation.pdf.gz | 422.8 KB | Display | wwPDB validaton report |
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Full document | 5c9y_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 5c9y_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5c9y_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/5c9y ftp://data.pdbj.org/pub/pdb/validation_reports/c9/5c9y | HTTPS FTP |
-Related structure data
Related structure data | 4ryvC 4y31C 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 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.86 % / Description: plate |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81738 Å |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jul 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81738 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 21584 / % possible obs: 99.5 % / Redundancy: 7.16 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.96 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 7.16 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.45 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ICX Resolution: 1.5→42.48 Å / Cross valid method: FREE R-VALUE Details: Flat postive electron densities could be observed in the structure indicating the presence of puring rings and tails of three trans-zeatin molecules: two inside protein cavity (one ...Details: Flat postive electron densities could be observed in the structure indicating the presence of puring rings and tails of three trans-zeatin molecules: two inside protein cavity (one interacting with Tyr82 and other with Ser101) and one on the surface of protein (staying in contact with Glu35). However they possess discontinuities and are insufficient for proper ligand modeling thus the structure is deposited without ligand molecules in its coordinates although trans-zeatin was present in crystallization condintions.
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Refinement step | Cycle: LAST / Resolution: 1.5→42.48 Å
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LS refinement shell | Highest resolution: 1.5 Å |