+Open data
-Basic information
Entry | Database: PDB / ID: 5xvj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of AL7 PAL domain | ||||||
Components | PHD finger protein ALFIN-LIKE 7 | ||||||
Keywords | GENE REGULATION / PRC1 interactor / Alfin-like family protein | ||||||
Function / homology | Function and homology information methylated histone binding / chromatin organization / transcription cis-regulatory region binding / regulation of DNA-templated transcription / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xvj.cif.gz | 75 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xvj.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/5xvj ftp://data.pdbj.org/pub/pdb/validation_reports/xv/5xvj | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15366.352 Da / Num. of mol.: 2 / Fragment: UNP residues 9-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AL7, At1g14510, F14L17.29, T5E21.1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q8LA16 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.84 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.2 M lithium sulfate, 0.1 M sodium phosphate/ Citric acid, pH 4.2, 20% (w/v) PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 4, 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: 1.4→50 Å / Num. obs: 42939 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 11.7 / Num. unique obs: 4268 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.277 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2.1 / Phase error: 19.27 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→38.277 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|