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Open data
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Basic information
Entry | Database: PDB / ID: 2qqg | ||||||
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Title | Hst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide | ||||||
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![]() | HYDROLASE / Hst2 / Sir2 / histone deacetylase / Metal-binding / NAD / Nucleus / Repressor / Transcription / Transcription regulation / Zinc | ||||||
Function / homology | ![]() Transcriptional activation of mitochondrial biogenesis / negative regulation of mitotic recombination / NAD-dependent histone H4K16 deacetylase activity / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones ...Transcriptional activation of mitochondrial biogenesis / negative regulation of mitotic recombination / NAD-dependent histone H4K16 deacetylase activity / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / NAD-dependent histone deacetylase activity / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / NAD+ binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / transferase activity / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marmorstein, R. / Sanders, B. / Zhao, K. / Slama, J. | ||||||
![]() | ![]() Title: Structural basis for nicotinamide inhibition and base exchange in sir2 enzymes. Authors: Sanders, B.D. / Zhao, K. / Slama, J.T. / Marmorstein, R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.9 KB | Display | ![]() |
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PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769.6 KB | Display | ![]() |
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Full document | ![]() | 776.8 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2od2C ![]() 2od7C ![]() 2od9C ![]() 2qqfC ![]() 1szdS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 34794.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HST2 / Plasmid: pRSET-A / Production host: ![]() ![]() References: UniProt: P53686, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Protein/peptide | Mass: 1310.615 Da / Num. of mol.: 1 / Fragment: sequence database residues 13-23 / Source method: obtained synthetically Details: The H4 peptide was chemically synthesized using standard solid phase synthesis chemistry. The peptide is naturally found in Saccharomyces cerevisiae. References: UniProt: P02309 |
-Non-polymers , 4 types, 119 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/A1R.gif)
![](data/chem/img/NCA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/A1R.gif)
![](data/chem/img/NCA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-A1R / |
#5: Chemical | ChemComp-NCA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.64 % |
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Crystal grow | Temperature: 298 K / pH: 5.6 Details: 2.0 M Ammonium Sulfate, 100 mM Na citrate, pH 5.6, 200 mM K/Na tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 16, 2006 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9777 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 27580 / % possible obs: 99.9 % / Observed criterion σ(I): 6.1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.111 / Rsym value: 0.117 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.32 / % possible all: 99.6 |
-Phasing
Phasing MR | Rfactor: 0.389 / Cor.coef. Fo:Fc: 0.658 / Cor.coef. Io to Ic: 0.404
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SZD Resolution: 2.05→28.34 Å / σ(F): 0
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Solvent computation | Bsol: 59.07 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→28.34 Å
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Xplor file |
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