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Yorodumi- PDB-5y53: Crystal structure of AL2 PAL domain in complex with AtBMI1b bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y53 | ||||||
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Title | Crystal structure of AL2 PAL domain in complex with AtBMI1b binding site | ||||||
Components |
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Keywords | GENE REGULATION / PRC1 interactor / alfin-like family protein / Complex | ||||||
Function / homology | Function and homology information response to water deprivation / protein autoubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / chromatin organization / histone binding / protein ubiquitination / regulation of DNA-templated transcription / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å | ||||||
Authors | Peng, L. / Wang, L.L. / Huang, Y. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch Authors: Peng, L. / Wang, L. / Zhang, Y. / Dong, A. / Shen, W.H. / Huang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y53.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y53.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 5y53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y53_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 5y53_full_validation.pdf.gz | 466.3 KB | Display | |
Data in XML | 5y53_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 5y53_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/5y53 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/5y53 | HTTPS FTP |
-Related structure data
Related structure data | 5xvjC 5xvlSC 5xvwC 5y21C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15508.561 Da / Num. of mol.: 4 / Fragment: UNP residues 10-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AL2, At3g11200, F11B9.12, F9F8.2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9SRM4 #2: Protein/peptide | Mass: 2153.509 Da / Num. of mol.: 2 / Fragment: UNP residues 269-286 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) References: UniProt: Q9M9Y4, RING-type E3 ubiquitin transferase #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: 2.14 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 2000 MME, 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.598→30 Å / Num. obs: 69212 / % possible obs: 98.6 % / Redundancy: 7.6 % / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 6945 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XVL Resolution: 1.598→28.603 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 16.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.598→28.603 Å
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Refine LS restraints |
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LS refinement shell |
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