+Open data
-Basic information
Entry | Database: PDB / ID: 4nj5 | ||||||
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Title | Crystal structure of SUVH9 | ||||||
Components | Probable histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH9 | ||||||
Keywords | METAL BINDING PROTEIN / SET domain / Zinc binding motif / Zinc binding | ||||||
Function / homology | Function and homology information gene silencing by siRNA-directed DNA methylation / : / DNA-mediated transformation / chromosome, centromeric region / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Du, J. / Patel, D.J. | ||||||
Citation | Journal: Nature / Year: 2014 Title: SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Authors: Johnson, L.M. / Du, J. / Hale, C.J. / Bischof, S. / Feng, S. / Chodavarapu, R.K. / Zhong, X. / Marson, G. / Pellegrini, M. / Segal, D.J. / Patel, D.J. / Jacobsen, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nj5.cif.gz | 207.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nj5.ent.gz | 165.2 KB | Display | PDB format |
PDBx/mmJSON format | 4nj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/4nj5 ftp://data.pdbj.org/pub/pdb/validation_reports/nj/4nj5 | HTTPS FTP |
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-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
#1: Protein | Mass: 58003.430 Da / Num. of mol.: 1 / Fragment: unp residues 134-650 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Gene: At4g13460, SDG22, SET22, SUVH9, T6G15.10 / Plasmid: pFastBac HTB / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9T0G7, histone-lysine N-methyltransferase | ||
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#2: Chemical | #3: 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: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.2823 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2012 |
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2823 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 21778 / Num. obs: 21408 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 35 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2136 / Rsym value: 0.698 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→49.679 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 22.77 / 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: 2.4→49.679 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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