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- PDB-4ld9: Crystal structure of the N-terminally acetylated BAH domain of Si... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ld9 | ||||||
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Title | Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle | ||||||
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![]() | NUCLEAR PROTEIN/TRANSCRIPTION/DNA / BETA BARREL / PROTEIN-DNA COMPLEX / DOUBLE HELIX / alpha-helix / beta-sheet / double stranded DNA / chromatin binding / chromatin / N-terminal acetylation / nucleus / NUCLEAR PROTEIN-TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / nuclear origin of replication recognition complex / chromatin silencing complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / DNA replication origin binding / subtelomeric heterochromatin formation / DNA replication initiation ...establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / nuclear origin of replication recognition complex / chromatin silencing complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / DNA replication origin binding / subtelomeric heterochromatin formation / DNA replication initiation / heterochromatin / nucleosome binding / heterochromatin formation / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / nucleosome assembly / single-stranded DNA binding / double-stranded DNA binding / nucleic acid binding / chromosome, telomeric region / protein heterodimerization activity / chromatin binding / nucleolus / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Arnaudo, N. / Fernandez, I.S. / McLaughlin, S.H. / Peak-Chew, S.Y. / Rhodes, D. / Martino, F. | ||||||
![]() | ![]() Title: The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle. Authors: Arnaudo, N. / Fernandez, I.S. / McLaughlin, S.H. / Peak-Chew, S.Y. / Rhodes, D. / Martino, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 397.6 KB | Display | ![]() |
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PDB format | ![]() | 318.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 530.6 KB | Display | ![]() |
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Full document | ![]() | 645.1 KB | Display | |
Data in XML | ![]() | 62.6 KB | Display | |
Data in CIF | ![]() | 86.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 5 types, 10 molecules AEBFCGDHKL
#1: Protein | Mass: 15421.101 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13965.265 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #7: Protein | Mass: 28073.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10 / Production host: ![]() ![]() |
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-Widom 601 sequence ... , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 51808.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence has been selected in vitro |
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#6: DNA chain | Mass: 51341.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence has been selected in vitro |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.55 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 6.5 Details: 50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 25, 2013 |
Radiation | Monochromator: don't know. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 44335 / Num. obs: 44335 / % possible obs: 90 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
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Processing
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Refinement | Resolution: 3.306→19.997 Å / SU ML: 0.69 / σ(F): 1.99 / Phase error: 36.76 / 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: 3.306→19.997 Å
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Refine LS restraints |
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LS refinement shell |
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