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Yorodumi- PDB-4twj: The structure of Sir2Af2 bound to a myristoylated histone peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 4twj | ||||||
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Title | The structure of Sir2Af2 bound to a myristoylated histone peptide | ||||||
Components |
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Keywords | HYDROLASE / Sirtuin / demyristoylation / archaeal proteins / histone peptide | ||||||
Function / homology | Function and homology information HDMs demethylate histones / HATs acetylate histones / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / replication fork protection complex ...HDMs demethylate histones / HATs acetylate histones / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / NAD+ binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / transferase activity / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ringel, A.E. / Roman, C. / Wolberger, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2014 Title: Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2. Authors: Ringel, A.E. / Roman, C. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4twj.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4twj.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 4twj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/4twj ftp://data.pdbj.org/pub/pdb/validation_reports/tw/4twj | HTTPS FTP |
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-Related structure data
Related structure data | 4twiC 1ma3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 28537.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: cobB2, Sir2Af2, AF_0112 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O30124, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Protein/peptide | Mass: 1795.269 Da / Num. of mol.: 1 / Fragment: UNP residues 9-21 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02309 |
-Non-polymers , 4 types, 208 molecules
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | ChemComp-ACT / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1 M Na-acetate pH 4.8, 14-18% (v/v) 2-propanol, and 14-15% (w/v) PEG 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→42.93 Å / Num. obs: 30123 / % possible obs: 99.73 % / Redundancy: 3.3 % / Rsym value: 0.05007 / Net I/σ(I): 13.24 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.15 / % possible all: 97.89 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MA3 Resolution: 1.65→42.93 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.769 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / 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: 19.8 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→42.93 Å
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