+Open data
-Basic information
Entry | Database: PDB / ID: 3fk3 | ||||||
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Title | Structure of the Yeats Domain, Yaf9 | ||||||
Components | Protein AF-9 homolog | ||||||
Keywords | TRANSCRIPTION / beta-sandwich / Activator / Chromatin regulator / DNA damage / DNA repair / Nucleus / Transcription regulation | ||||||
Function / homology | Function and homology information Swr1 complex / NuA4 histone acetyltransferase complex / subtelomeric heterochromatin formation / histone binding / chromosome, telomeric region / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin ...Swr1 complex / NuA4 histone acetyltransferase complex / subtelomeric heterochromatin formation / histone binding / chromosome, telomeric region / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Wang, A.Y. / Schulze, J.M. / Skordalakes, E. / Berger, J.M. / Rine, J. / Kobor, M.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation Authors: Wang, A.Y. / Schulze, J.M. / Skordalakes, E. / Gin, J.W. / Berger, J.M. / Rine, J. / Kobor, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fk3.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fk3.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fk3_validation.pdf.gz | 438 KB | Display | wwPDB validaton report |
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Full document | 3fk3_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 3fk3_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 3fk3_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/3fk3 ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fk3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 19017.979 Da / Num. of mol.: 3 / Fragment: YEATS domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: N1966, YAF9, YNL107W / Production host: Escherichia coli (E. coli) / References: UniProt: P53930 #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: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7.5 Details: 10% PEG 3350, 100 mM Na, Tartrate, 20% glycerol, pH 7.5, microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587, 0.9795, 1.0199 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2004 | ||||||||||||
Radiation | Monochromator: KHOZU Double flat crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→20 Å / Num. obs: 24936 / % possible obs: 95.8 % / Observed criterion σ(F): 3 / Redundancy: 6.3 % / Rsym value: 0.063 | ||||||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 5 % / Rsym value: 0.368 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.958 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.237 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.672 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 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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