+Open data
-Basic information
Entry | Database: PDB / ID: 5yc3 | ||||||
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Title | Crystal structure of AL3 PHD finger bound to H3K4me2 | ||||||
Components |
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Keywords | TRANSCRIPTION / PHD finger | ||||||
Function / homology | Function and homology information chromocenter / plastid / transcription coregulator activity / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription cis-regulatory region binding / protein heterodimerization activity / regulation of DNA-templated transcription ...chromocenter / plastid / transcription coregulator activity / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription cis-regulatory region binding / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å | ||||||
Authors | Zhao, S. / Zhang, B. / Li, H. | ||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Systematic Profiling of Histone Readers in Arabidopsis thaliana. Authors: Zhao, S. / Zhang, B. / Yang, M. / Zhu, J. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yc3.cif.gz | 29.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yc3.ent.gz | 16.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/5yc3 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5yc3 | HTTPS FTP |
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-Related structure data
Related structure data | 5y20C 5yc4C 2fsaS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 6528.371 Da / Num. of mol.: 1 / Fragment: PHD finger, UNP residues 191-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AL3, At3g42790, T21C14_10 / Plasmid: pGEX6p / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9M2B4 | ||
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#2: Protein/peptide | Mass: 1090.300 Da / Num. of mol.: 1 / Fragment: H3 peptide 1-15 / Mutation: K4 dimethylation / Source method: obtained synthetically / Details: chemically synthesized H3K4me2 peptide / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226*PLUS | ||
#3: Chemical | #4: 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: 2.46 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic, pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2016 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 2763 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 34.31 Å2 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.053 / Rrim(I) all: 0.197 / Χ2: 1.195 / Net I/σ(I): 4.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FSA Resolution: 2.601→39.257 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 66.27 Å2 / Biso mean: 34.2109 Å2 / Biso min: 20.29 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.601→39.257 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %
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