+Open data
-Basic information
Entry | Database: PDB / ID: 5czy | ||||||
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Title | Crystal structure of LegAS4 | ||||||
Components | Legionella effector LegAS4 | ||||||
Keywords | TRANSFERASE / SET domain | ||||||
Function / homology | Function and homology information histone H3K36 methyltransferase activity / regulation of DNA-templated transcription / chromatin Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Model details | complexed with PL-74 | ||||||
Authors | Son, J. / Hwang, K.Y. / Lee, W.C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: Crystal structure of Legionella pneumophila type IV secretion system effector LegAS4 Authors: Son, J. / Jo, C.H. / Murugan, R.N. / Bang, J.K. / Hwang, K.Y. / Lee, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5czy.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5czy.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 5czy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5czy_validation.pdf.gz | 794.6 KB | Display | wwPDB validaton report |
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Full document | 5czy_full_validation.pdf.gz | 796.4 KB | Display | |
Data in XML | 5czy_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 5czy_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/5czy ftp://data.pdbj.org/pub/pdb/validation_reports/cz/5czy | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 55533.492 Da / Num. of mol.: 1 / Fragment: UNP residues 63-545 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Strain: Philadelphia 1 / Gene: legAS4 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZUS4 | ||||
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#2: Chemical | #3: Chemical | ChemComp-SAM / | #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: 49.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M sodium citrate, 15 % (v/v) isopropanol, 10%(w/v) PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→66.832 Å / Num. obs: 28465 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.21 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.071 / Χ2: 0.977 / Net I/σ(I): 29.36 / Num. measured all: 490905 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Starting model: SAD Resolution: 2.2→66.832 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→66.832 Å
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Refine LS restraints |
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LS refinement shell |
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