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Yorodumi- PDB-1q1a: Structure of the yeast Hst2 protein deacetylase in ternary comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q1a | ||||||
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Title | Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide | ||||||
Components |
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Keywords | GENE REGULATION / ternary complex / histone deacetylase / 2'-O-ADP ribose | ||||||
Function / homology | Function and homology information 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 / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / 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 / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / 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 / Oxidative Stress Induced Senescence / replication fork protection complex / 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 / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Zhao, K. / Chai, X. / Marmorstein, R. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-Acetyl ADP ribose and histone peptide. Authors: Zhao, K. / Chai, X. / Marmorstein, R. #1: Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure and autoregulation of the yeast Hst2 homolog of Sir2 Authors: Zhao, K. / Chai, X. / Clements, A. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q1a.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q1a.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/1q1a ftp://data.pdbj.org/pub/pdb/validation_reports/q1/1q1a | HTTPS FTP |
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-Related structure data
Related structure data | 1q17C 1q14S S: Starting model for refinement C: citing same article (ref.) |
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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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Details | protein is a monomer upon the substrate binding |
-Components
#1: Protein | Mass: 32654.424 Da / Num. of mol.: 1 / Fragment: C-terminla deletion of hst2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P53686 |
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#2: Protein/peptide | Mass: 1197.457 Da / Num. of mol.: 1 / Fragment: Residues 12-21 / Source method: obtained synthetically / Details: chemically synthesized / References: UniProt: P02309 |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-OAD / |
#5: 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: 2.13 Å3/Da / Density % sol: 42.14 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4K, , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2003 |
Radiation | Monochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 43331 / Num. obs: 42619 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.045 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4192 / Rsym value: 0.163 / % possible all: 93.9 |
Reflection | *PLUS Num. obs: 43331 |
Reflection shell | *PLUS % possible obs: 93.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q14 Resolution: 1.5→29.74 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.5557 Å2 / ksol: 0.385886 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.18 Å / Luzzati sigma a free: 0.1 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→29.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.5 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.209 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.231 / Rfactor Rwork: 0.218 |