+Open data
-Basic information
Entry | Database: PDB / ID: 4psw | ||||||
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Title | Crystal structure of histone acetyltransferase complex | ||||||
Components |
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Keywords | TRANSFERASE / HAT WD40 / histone acetyltransferase / AcCoA / Phosphorylation / Cytoplasmatic | ||||||
Function / homology | Function and homology information HATs acetylate histones / Rpd3L complex / Rpd3L-Expanded complex / HDACs deacetylate histones / histone H4 acetyltransferase activity / NuRD complex / ESC/E(Z) complex / RMTs methylate histone arginines / histone acetyltransferase complex / subtelomeric heterochromatin formation ...HATs acetylate histones / Rpd3L complex / Rpd3L-Expanded complex / HDACs deacetylate histones / histone H4 acetyltransferase activity / NuRD complex / ESC/E(Z) complex / RMTs methylate histone arginines / histone acetyltransferase complex / subtelomeric heterochromatin formation / histone acetyltransferase activity / nucleosome binding / histone acetyltransferase / DNA-templated transcription initiation / nucleosome / chromatin organization / histone binding / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / DNA repair / chromatin binding / host cell nucleus / regulation of DNA-templated transcription / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Ophiophagus hannah (king cobra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å | ||||||
Authors | Yang, M. / Li, Y. | ||||||
Citation | Journal: Genes Dev. / Year: 2014 Title: Hat2p recognizes the histone H3 tail to specify the acetylation of the newly synthesized H3/H4 heterodimer by the Hat1p/Hat2p complex Authors: Li, Y. / Zhang, L. / Liu, T. / Chai, C. / Fang, Q. / Wu, H. / Agudelo garcia, P.A. / Han, Z. / Zong, S. / Yu, Y. / Zhang, X. / Parthun, M.R. / Chai, J. / Xu, R.M. / Yang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4psw.cif.gz | 303.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4psw.ent.gz | 253.9 KB | Display | PDB format |
PDBx/mmJSON format | 4psw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4psw_validation.pdf.gz | 736.7 KB | Display | wwPDB validaton report |
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Full document | 4psw_full_validation.pdf.gz | 746.2 KB | Display | |
Data in XML | 4psw_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 4psw_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/4psw ftp://data.pdbj.org/pub/pdb/validation_reports/ps/4psw | 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: 37276.992 Da / Num. of mol.: 1 / Fragment: UNP residues 4-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: HAT1, YPL001W, LPA16W, YP8132.12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12341, histone acetyltransferase |
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#2: Protein | Mass: 45187.879 Da / Num. of mol.: 1 / Fragment: UNP residues 7-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: HAT2, YEL056W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P39984 |
#3: Protein/peptide | Mass: 4133.991 Da / Num. of mol.: 1 / Fragment: UNP residues 8-45 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ophiophagus hannah (king cobra) / Gene: H4-VIII, L345_01081 / Production host: Escherichia coli (E. coli) / References: UniProt: V8PGJ1 |
#4: Chemical | ChemComp-COA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M potassium sodium tartrate and 20%(w/v) polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.7 Å / Num. all: 56511 / Num. obs: 56511 / % possible obs: 99.8 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1.34 |
Reflection shell | Resolution: 2.1→29.7 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→29.7 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.88 / 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: 2.101→29.7 Å
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Refine LS restraints |
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LS refinement shell |
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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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