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- PDB-1mj9: Crystal structure of yeast Esa1(C304S) mutant complexed with Coen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mj9 | ||||||
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Title | Crystal structure of yeast Esa1(C304S) mutant complexed with Coenzyme A | ||||||
![]() | ESA1 PROTEIN | ||||||
![]() | TRANSFERASE / Esa1 / HAT / Histone acetyltransferase / MYST | ||||||
Function / homology | ![]() DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / DNA-templated transcription elongation / positive regulation of triglyceride biosynthetic process / histone H4 acetyltransferase activity / rDNA heterochromatin formation ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / DNA-templated transcription elongation / positive regulation of triglyceride biosynthetic process / histone H4 acetyltransferase activity / rDNA heterochromatin formation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / peptide N-acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / NuA4 histone acetyltransferase complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / nucleosome / regulation of cell cycle / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yan, Y. / Harper, S. / Speicher, D. / Marmorstein, R. | ||||||
![]() | ![]() Title: The catalytic mechanism of the ESA1 histone acetyltransferase involves a self-acetylated intermediate. Authors: Yan, Y. / Harper, S. / Speicher, D.W. / Marmorstein, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.3 KB | Display | ![]() |
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Full document | ![]() | 457.6 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mjaC ![]() 1mjbC ![]() 1fy7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33356.352 Da / Num. of mol.: 1 Fragment: HISTONE ACETYLTRANSFERASE DOMAIN (Residues 160-445) Mutation: C304S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: YOR244W / Plasmid: PRSET-A / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-COA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.94 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium cacodylate, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2001 / Details: mirrors |
Radiation | Monochromator: silicon and germanium crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 17817 / Num. obs: 17817 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25.6 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 7 / Num. unique all: 1743 / Rsym value: 0.316 / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 17931 / Num. measured all: 456785 / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS Rmerge(I) obs: 0.316 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1FY7 Resolution: 2.5→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.52 Å /
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.232 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.327 / Rfactor Rwork: 0.248 |