+Open data
-Basic information
Entry | Database: PDB / ID: 3dm7 | ||||||
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Title | Crystal Structure of the Vps75 Histone Chaperone | ||||||
Components | Vacuolar protein sorting-associated protein 75 | ||||||
Keywords | CHAPERONE / Vps75 (vacuolar protein sorting 75) / NAP1 / histone chaperone / Nucleus / Phosphoprotein / Protein transport / Transport | ||||||
Function / homology | Function and homology information H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / protein transport / nucleosome assembly / histone binding / chromatin binding / chromatin / identical protein binding ...H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / protein transport / nucleosome assembly / histone binding / chromatin binding / chromatin / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Tang, Y. / Marmorstein, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Structure of Vps75 and implications for histone chaperone function. Authors: Tang, Y. / Meeth, K. / Jiang, E. / Luo, C. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dm7.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dm7.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 3dm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dm7_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 3dm7_full_validation.pdf.gz | 439.3 KB | Display | |
Data in XML | 3dm7_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3dm7_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/3dm7 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/3dm7 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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: 27801.092 Da / Num. of mol.: 2 / Mutation: I80M, I160M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPS75, YNL246W, N0890 / Plasmid: modified pRSF-GST fusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P53853 #2: 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: 3 Å3/Da / Density % sol: 58.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 25% PEG4000, 100 mM MES, 0.2 M malic acid, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9789,0.9791,0.9537 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 13, 2007 / Details: mirrors | ||||||||||||
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. obs: 45182 / % possible obs: 99.1 % / Observed criterion σ(I): -3.5 / Redundancy: 13.8 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.096 / Net I/σ(I): 24.4 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 11 % / Mean I/σ(I) obs: 5.48 / Rsym value: 0.414 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.5 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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