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Yorodumi- PDB-4rkg: Structure of the MSL2 CXC domain bound with a non-specific (GC)6 DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rkg | ||||||
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Title | Structure of the MSL2 CXC domain bound with a non-specific (GC)6 DNA | ||||||
Components |
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Keywords | DNA binding protein/DNA / Zinc cluster / DNA binding domain / Dosage compensation / DNA binding protein-DNA complex | ||||||
Function / homology | Function and homology information dosage compensation complex / histone H2B ubiquitin ligase activity / X chromosome located dosage compensation complex, transcription activating / X chromosome / HATs acetylate histones / protein-RNA adaptor activity / MSL complex / dosage compensation by hyperactivation of X chromosome / sex-chromosome dosage compensation / chromatin-protein adaptor activity ...dosage compensation complex / histone H2B ubiquitin ligase activity / X chromosome located dosage compensation complex, transcription activating / X chromosome / HATs acetylate histones / protein-RNA adaptor activity / MSL complex / dosage compensation by hyperactivation of X chromosome / sex-chromosome dosage compensation / chromatin-protein adaptor activity / lncRNA binding / nuclear chromosome / protein localization to chromatin / molecular condensate scaffold activity / RING-type E3 ubiquitin transferase / protein polyubiquitination / chromosome / ubiquitin protein ligase activity / sequence-specific double-stranded DNA binding / protein ubiquitination / chromatin binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zheng, S. / Ye, K. | ||||||
Citation | Journal: Genes Dev. / Year: 2014 Title: Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation. Authors: Zheng, S. / Villa, R. / Wang, J. / Feng, Y. / Wang, J. / Becker, P.B. / Ye, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rkg.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rkg.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4rkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rkg_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 4rkg_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 4rkg_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 4rkg_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/4rkg ftp://data.pdbj.org/pub/pdb/validation_reports/rk/4rkg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 5652.500 Da / Num. of mol.: 2 / Fragment: CXC domain (UNP RESIDUES 520-570) / Mutation: C560G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3241, msl-2, MSL2 / Plasmid: pET28a-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: P50534, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: DNA chain | Mass: 3665.368 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-ZN / |
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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: 3.18 Å3/Da / Density % sol: 61.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES-Na (pH 7.5), 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97913 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97913 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 8732 / Num. obs: 8584 / % possible obs: 98.3 % / Observed criterion σ(I): 6.5 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.699 / Num. unique all: 416 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→18.015 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 34.7 / 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: 2.5→18.015 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 17.3669 Å / Origin y: 0.2768 Å / Origin z: 18.9614 Å
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Refinement TLS group | Selection details: ALL |