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- PDB-1mjb: Crystal structure of yeast Esa1 histone acetyltransferase E338Q m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mjb | ||||||
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Title | Crystal structure of yeast Esa1 histone acetyltransferase E338Q mutant complexed with acetyl coenzyme A | ||||||
![]() | Esa1 protein | ||||||
![]() | TRANSFERASE / Esa1 / histone acetyltransferases / HAT / 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 | ![]() | 69.7 KB | Display | ![]() |
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PDB format | ![]() | 56.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450 KB | Display | ![]() |
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Full document | ![]() | 454.6 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mj9C ![]() 1mjaC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 33387.430 Da / Num. of mol.: 1 Fragment: Histone acetyltransferase domain (Residues 160-445) Mutation: E338Q 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-ACO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.17 % | ||||||||||||||||||||||||||||||
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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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 11, 2001 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 17458 / Num. obs: 17458 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3 / Num. unique all: 1701 / Rsym value: 0.291 / % possible all: 96.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 18056 / Num. measured all: 162442 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Rmerge(I) obs: 0.291 |
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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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LS refinement shell | Resolution: 2.5→2.52 Å /
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.232 / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.229 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.288 / Rfactor Rwork: 0.283 |