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Yorodumi- PDB-1pu9: Crystal Structure of Tetrahymena GCN5 with Bound Coenzyme A and a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pu9 | ||||||
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Title | Crystal Structure of Tetrahymena GCN5 with Bound Coenzyme A and a 19-residue Histone H3 Peptide | ||||||
Components |
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Keywords | TRANSFERASE/STRUCTURAL PROTEIN / HISTONE ACETYLTRANSFERASE / GCN5-RELATED N-ACETYLTRANSFERASE / COA-BINDING PROTEIN / TERNARY COMPLEX / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information chromatin organization => GO:0006325 / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / 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 / histone H3 acetyltransferase activity ...chromatin organization => GO:0006325 / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / 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 / histone H3 acetyltransferase activity / replication fork protection complex / Oxidative Stress Induced Senescence / ATAC complex / 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 / rRNA transcription / CENP-A containing nucleosome / intracellular copper ion homeostasis / histone acetyltransferase / aerobic respiration / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Clements, A. / Poux, A.N. / Lo, W.S. / Pillus, L. / Berger, S.L. / Marmorstein, R. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Structural basis for histone and phospho-histone binding by the GCN5 histone acetyltransferase Authors: Clements, A. / Poux, A.N. / Lo, W.S. / Pillus, L. / Berger, S.L. / Marmorstein, R. | ||||||
History |
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Remark 999 | SEQUENCE The author state: " This construct was cloned directly from the Tetrahymena thermophilia ...SEQUENCE The author state: " This construct was cloned directly from the Tetrahymena thermophilia genome. It is assumed that the protein sequence is correct, particularly in the case of the phenylalanine, as it is highly conserved among Gcn5 histone acetyltransferases from other species." |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pu9.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pu9.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pu9_validation.pdf.gz | 452.7 KB | Display | wwPDB validaton report |
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Full document | 1pu9_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 1pu9_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1pu9_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/1pu9 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/1pu9 | HTTPS FTP |
-Related structure data
Related structure data | 1puaC 1q2cC 1qsnS 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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-Components
#1: Protein | Mass: 19457.658 Da / Num. of mol.: 1 / Fragment: residues 48-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Plasmid: PRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: Q27198 |
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#2: Protein/peptide | Mass: 2019.352 Da / Num. of mol.: 1 / Fragment: Residues 305-323 / Source method: obtained synthetically Details: This protein naturally occurs in Saccharomyces cerevisiae (Baker's yeast). References: UniProt: P02303, UniProt: P61830*PLUS |
#3: Chemical | ChemComp-COA / |
#4: 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: 2.71 Å3/Da / Density % sol: 54.68 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: Ammonium sulfate, MnCl2, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9213 |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 8, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9213 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→27 Å / Num. obs: 10007 / % possible obs: 96 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.4 Å2 |
Reflection shell | Resolution: 2.24→2.39 Å |
Reflection | *PLUS Highest resolution: 2.21 Å / Lowest resolution: 50 Å / Num. obs: 22051 / % possible obs: 99.5 % / Num. measured all: 67990 / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS Highest resolution: 2.21 Å / Lowest resolution: 2.35 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 1.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QSN Resolution: 2.3→21.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1492487.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.19 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→21.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.232 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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