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Yorodumi- PDB-1ml9: Structure of the Neurospora SET domain protein DIM-5, a histone l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ml9 | ||||||
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Title | Structure of the Neurospora SET domain protein DIM-5, a histone lysine methyltransferase | ||||||
Components | Histone H3 methyltransferase DIM-5 | ||||||
Keywords | TRANSFERASE / DIM-5 / AdoMet-dependent Methyltransferase Histone H3 Lysine-9 Methylation | ||||||
Function / homology | Function and homology information [histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / histone methyltransferase activity / chromosome / methylation / double-stranded DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Neurospora crassa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å | ||||||
Authors | Zhang, X. / Tamaru, H. / Khan, S.I. / Horton, J.R. / Keefe, L.J. / Selker, E.U. / Cheng, X. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase Authors: Zhang, X. / Tamaru, H. / Khan, S.I. / Horton, J.R. / Keefe, L.J. / Selker, E.U. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ml9.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ml9.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ml9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ml9_validation.pdf.gz | 364.4 KB | Display | wwPDB validaton report |
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Full document | 1ml9_full_validation.pdf.gz | 369.9 KB | Display | |
Data in XML | 1ml9_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1ml9_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/1ml9 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/1ml9 | 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
#1: Protein | Mass: 34111.551 Da / Num. of mol.: 1 / Fragment: Residues 17-318 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa (fungus) / Plasmid: pXC379 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: GenBank: 17063801, UniProt: Q8X225*PLUS, histone-lysine N-methyltransferase | ||||
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#2: Chemical | #3: Chemical | ChemComp-UNK / #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: 2.22 Å3/Da / Density % sol: 44.65 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium sulfate, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 9.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0332, 1.2834, 1.2830 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 10, 2002 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.98→24.83 Å / Num. all: 20963 / Num. obs: 20963 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.37 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 15.4 | ||||||||||||
Reflection shell | Resolution: 1.98→2.02 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1011 / Rsym value: 0.276 / % possible all: 95.8 | ||||||||||||
Reflection | *PLUS % possible obs: 97 % / Num. measured all: 112569 / Rmerge(I) obs: 0.055 | ||||||||||||
Reflection shell | *PLUS % possible obs: 95.8 % / Rmerge(I) obs: 0.276 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.98→24.83 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 32.3 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 24.83 Å / Luzzati sigma a obs: 0.23 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→24.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.1 Å / Rfactor Rfree error: 0.015
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Refinement | *PLUS Rfactor Rfree: 0.258 / Rfactor Rwork: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.281 / Rfactor Rwork: 0.266 |