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Yorodumi- PDB-4lct: Crystal Structure and Versatile Functional Roles of the COP9 Sign... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lct | ||||||
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Title | Crystal Structure and Versatile Functional Roles of the COP9 Signalosome Subunit 1 | ||||||
Components | COP9 signalosome complex subunit 1 | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information response to absence of light / red, far-red light phototransduction / protein deneddylation / embryo development ending in seed dormancy / COP9 signalosome / hyperosmotic response / response to salt stress / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Lee, J.-H. / Yi, L. / Li, J. / Schweitzer, K. / Borgmann, M. / Naumann, M. / Wu, H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Crystal structure and versatile functional roles of the COP9 signalosome subunit 1. Authors: Lee, J.H. / Yi, L. / Li, J. / Schweitzer, K. / Borgmann, M. / Naumann, M. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lct.cif.gz | 269 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lct.ent.gz | 220.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/4lct ftp://data.pdbj.org/pub/pdb/validation_reports/lc/4lct | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39879.695 Da / Num. of mol.: 4 / Fragment: UNP residues 32-379 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSN1, COP11, FUS6, At3g61140, T20K12.40 / Production host: Escherichia coli (E. coli) / References: UniProt: P45432 #2: Chemical | ChemComp-SO4 / #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: 3.55 Å3/Da / Density % sol: 65.39 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 7 Details: 0.1M BTP pH 7.0, 0.2M ammonium sulfate, 10% (w/v) polyethylene glycol 8000, 5mM dithiothreitol, VAPOR DIFFUSION, temperature 293.15K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48.7 Å / Num. obs: 61556 / % possible obs: 26.7 % / Observed criterion σ(F): 4.1 / Observed criterion σ(I): 4.1 |
Reflection shell | Highest resolution: 2.7 Å / % possible all: 99.73 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→48.7 Å / SU ML: 0.49 / σ(F): 1.36 / Phase error: 29.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.122 Å2 / ksol: 0.365 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→48.7 Å
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Refine LS restraints |
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LS refinement shell |
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