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Yorodumi- PDB-3ob9: Structure of the human MSL3 chromo-barrel domain at 2.5 Angstrom ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ob9 | ||||||
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Title | Structure of the human MSL3 chromo-barrel domain at 2.5 Angstrom resolution | ||||||
Components | Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c | ||||||
Keywords | Transcription Regulator / chromodomain / chromo-barrel / chromo / methyllysine binding / histone tail / nucleosome recognition / Histone H4K20Me1 / nucleus | ||||||
Function / homology | Function and homology information : / : / : / heterochromatin formation => GO:0031507 / : / MSL complex / : / histone H4K16 acetyltransferase activity / NuA4 histone acetyltransferase complex / histone acetyltransferase complex ...: / : / : / heterochromatin formation => GO:0031507 / : / MSL complex / : / histone H4K16 acetyltransferase activity / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / methylated histone binding / HATs acetylate histones / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Moore, S.A. / Ferhatoglu, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure of the human MSL3 chromo-barrel domain at 2.5 Angstrom resolution Authors: Moore, S.A. / Ferhatoglu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ob9.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ob9.ent.gz | 155 KB | Display | PDB format |
PDBx/mmJSON format | 3ob9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/3ob9 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/3ob9 | HTTPS FTP |
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-Related structure data
Related structure data | 2f5kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11231.825 Da / Num. of mol.: 5 / Fragment: hmsl3 (UNP residues 2 to 93) Source method: isolated from a genetically manipulated source Details: Bam HI/Eco RI MCS / Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_401190, MSL3, MSL3L1 / Plasmid: PGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A6NHW8, UniProt: Q8N5Y2*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.5 Å3/Da / Density % sol: 50.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.0 Ammonium Sulfate, 100 mM CHES pH 9.0, , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 22, 2009 / Details: Si 111 monochromator and focusing mirrors |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 19711 / Num. obs: 19514 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 56.7 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 16.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2F5K Resolution: 2.5→29.4 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.892 / SU B: 21.713 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.605 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.504→2.568 Å / Total num. of bins used: 20
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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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