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Yorodumi- PDB-5y21: Crystal structure of AL2 PAL domain in complex with AtRing1a prox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y21 | ||||||
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Title | Crystal structure of AL2 PAL domain in complex with AtRing1a proximal site | ||||||
Components |
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Keywords | GENE REGULATION / PRC1 interactor / Alfin-like family protein / Complex | ||||||
Function / homology | Function and homology information maintenance of floral meristem identity / maintenance of inflorescence meristem identity / maintenance of shoot apical meristem identity / seed germination / PRC1 complex / root development / cell fate determination / negative regulation of gene expression, epigenetic / RING-type E3 ubiquitin transferase / chromatin organization ...maintenance of floral meristem identity / maintenance of inflorescence meristem identity / maintenance of shoot apical meristem identity / seed germination / PRC1 complex / root development / cell fate determination / negative regulation of gene expression, epigenetic / RING-type E3 ubiquitin transferase / chromatin organization / histone binding / transferase activity / protein ubiquitination / negative regulation of DNA-templated transcription / 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: 1.769 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 | 5y21.cif.gz | 137.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y21.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 5y21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y21_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 5y21_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 5y21_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 5y21_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/5y21 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/5y21 | HTTPS FTP |
-Related structure data
Related structure data | 5xvjC 5xvlSC 5xvwC 5y53C 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
#1: Protein | Mass: 15508.561 Da / Num. of mol.: 2 / 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: 1823.156 Da / Num. of mol.: 2 / Fragment: UNP residues 307-320 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: F4K8U4, UniProt: Q9FKW0*PLUS #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: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG2000 MME, 0.1 M Tris, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97907 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 1.769→50 Å / Num. obs: 31734 / % possible obs: 99.3 % / Redundancy: 3.7 % / Net I/σ(I): 35.4 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 14.4 / Num. unique obs: 3179 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XVL Resolution: 1.769→27.791 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.769→27.791 Å
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Refine LS restraints |
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LS refinement shell |
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