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Yorodumi- PDB-5kwn: The WD domain ofArabidopsis thaliana E3 Ubiquitin Ligase COP1 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kwn | ||||||
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Title | The WD domain ofArabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide from HY5 | ||||||
Components |
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Keywords | Ligase/Peptide / photomorphogenesis E3 ligase WD domain transcription factor / Ligase-Peptide complex | ||||||
Function / homology | Function and homology information positive regulation of anthocyanin metabolic process / red or far-red light signaling pathway / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / response to red light / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / positive gravitropism / skotomorphogenesis ...positive regulation of anthocyanin metabolic process / red or far-red light signaling pathway / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / response to red light / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / positive gravitropism / skotomorphogenesis / photoperiodism, flowering / gibberellic acid mediated signaling pathway / red, far-red light phototransduction / response to far red light / photomorphogenesis / regulation of stomatal movement / nuclear ubiquitin ligase complex / response to abscisic acid / entrainment of circadian clock / positive regulation of circadian rhythm / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / abscisic acid-activated signaling pathway / response to cold / protein-DNA complex / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / DNA-binding transcription factor activity / DNA repair / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) Arabidopsis (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Uljon, S. / Blacklow, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The COP1 WD domain in complex with HY5 peptide Authors: Uljon, S. / Blacklow, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kwn.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kwn.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kwn_validation.pdf.gz | 429.2 KB | Display | wwPDB validaton report |
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Full document | 5kwn_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 5kwn_validation.xml.gz | 17 KB | Display | |
Data in CIF | 5kwn_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/5kwn ftp://data.pdbj.org/pub/pdb/validation_reports/kw/5kwn | HTTPS FTP |
-Related structure data
Related structure data | 5igoS S: Starting model for refinement |
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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 on special symmetry positions |
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Details | dimer of protein and peptide, according to gel filtration |
-Components
#1: Protein | Mass: 38165.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: COP1, At2g32950, T21L14.11 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P43254, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein/peptide | Mass: 2091.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant) / References: UniProt: O24646*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: Sodium Chloride 0.3M Hepes 7.2 0.1M PEG 3350 25% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→38.775 Å / Num. obs: 66069 / % possible obs: 99 % / Redundancy: 2.9 % / Net I/σ(I): 22.97 |
Reflection shell | Resolution: 1.42→1.471 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.1526 / Mean I/σ(I) obs: 6.09 / CC1/2: 0.992 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IGO Resolution: 1.42→38.775 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→38.775 Å
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Refine LS restraints |
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LS refinement shell |
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