+Open data
-Basic information
Entry | Database: PDB / ID: 2rim | ||||||
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Title | Crystal structure of Rtt109 | ||||||
Components | Regulator of Ty1 transposition protein 109 | ||||||
Keywords | TRANSFERASE / Rtt109 structure / DNA damage / DNA repair / Nucleus / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / replication-born double-strand break repair via sister chromatid exchange / retrotransposon silencing / histone H3 acetyltransferase activity ...histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / replication-born double-strand break repair via sister chromatid exchange / retrotransposon silencing / histone H3 acetyltransferase activity / histone H3K27 acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / histone acetyltransferase / protein modification process / nucleosome assembly / regulation of gene expression / DNA damage response / regulation of transcription by RNA polymerase II / chromatin / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Yuan, Y.A. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Structural insights into histone h3 lysine 56 acetylation by rtt109 Authors: Lin, C. / Yuan, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rim.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rim.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 2rim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rim_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
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Full document | 2rim_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 2rim_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 2rim_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/2rim ftp://data.pdbj.org/pub/pdb/validation_reports/ri/2rim | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52747.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RTT109, KIM2, REM50 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q07794 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG550 MME, Ammonium citrate, glycerol, Tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 16, 2007 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. all: 29160 / Num. obs: 30288 / % possible obs: 0.989 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.098 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.7 % / Rsym value: 0.541 / % possible all: 0.971 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→46.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.035 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.197 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.504 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→46.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.078→2.132 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.3684 Å / Origin y: 30.7892 Å / Origin z: 15.256 Å
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Refinement TLS group |
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