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Yorodumi- PDB-4nbm: Crystal structure of UVB photoreceptor UVR8 and light-induced str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nbm | ||||||
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Title | Crystal structure of UVB photoreceptor UVR8 and light-induced structural changes at 180K | ||||||
Components | Ultraviolet-B receptor UVR8 | ||||||
Keywords | GENE REGULATION / 7-blade beta-propeller | ||||||
Function / homology | Function and homology information entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding ...entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AND DIFFERENCE FOURIER FOR LIIGHT-INDUCED STRUCTURAL CHANGES / Resolution: 1.61 Å | ||||||
Authors | Yang, X. / Zeng, X. / Zhao, K.-H. / Ren, Z. | ||||||
Citation | Journal: Nat Plants / Year: 2015 Title: Dynamic Crystallography Reveals Early Signalling Events in Ultraviolet Photoreceptor UVR8. Authors: Zeng, X. / Ren, Z. / Wu, Q. / Fan, J. / Peng, P.P. / Tang, K. / Zhang, R. / Zhao, K.H. / Yang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nbm.cif.gz | 609.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nbm.ent.gz | 500.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nbm_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
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Full document | 4nbm_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 4nbm_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 4nbm_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/4nbm ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nbm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40875.438 Da / Num. of mol.: 4 / Fragment: UNP residues 13-382 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g63860, MGI19.7, UVR8 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9FN03 #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 290 K / pH: 9.2 Details: protein concentration 8mg/ml, mother liquor 0.1M MgCl2, 15-18% PEG8000 and 0.1M Tris HCl (pH 9.2), VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 5, 2013 |
Radiation | Monochromator: DIAMOND LAUE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→50 Å / Num. obs: 185277 / % possible obs: 87.9 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.038 |
-Processing
Software |
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Refinement | Method to determine structure: AND DIFFERENCE FOURIER FOR LIIGHT-INDUCED STRUCTURAL CHANGES Resolution: 1.61→29.86 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 20.62 / Stereochemistry target values: ML Details: THE AUTHOR STATES THAT ENTRIES 4NAA, 4NBM, AND 4NC4 WERE DERIVED FROM DYNAMIC CRYSTALLOGRAPHIC DATA SETS. SPECIFICALLY, EACH ENTRY PROVIDES THREE ASPECTS OF EXPERIMENTAL DATA THAT ARE NEEDED ...Details: THE AUTHOR STATES THAT ENTRIES 4NAA, 4NBM, AND 4NC4 WERE DERIVED FROM DYNAMIC CRYSTALLOGRAPHIC DATA SETS. SPECIFICALLY, EACH ENTRY PROVIDES THREE ASPECTS OF EXPERIMENTAL DATA THAT ARE NEEDED TO REPRODUCE AND VALIDATE OUR SCIENTIFIC FINDINGS. THEY INCLUDE: A) COORDINATES OF THE REFERENCE "DARK" STRUCTURE AS WE HAD DEPOSITED IN PDB; B) STRUCTURE FACTOR AMPLITUDES ACQUIRED IN THE "DARK" STATE; AND C) STRUCTURE FACTOR AMPLITUDES ACQUIRED IN THE "LIGHT" STATE. DATA SETS B) AND C) WERE COLLECTED FROM THE SAME CRYSTAL. OUR DEPOSITED MTZ FILE THUS CONTAINS DATA FROM BOTH B) AND C), AS WELL AS CALCULATED PHASES FROM A), WITH WHICH PDB USERS ARE ABLE TO GENERATE DIFFERENCE FOURIER MAPS TO EXAMINE LIGHT-INDUCED STRUCTURAL CHANGES.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→29.86 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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