+Open data
-Basic information
Entry | Database: PDB / ID: 1m1d | ||||||
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Title | TETRAHYMENA GCN5 WITH BOUND BISUBSTRATE ANALOG INHIBITOR | ||||||
Components |
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Keywords | TRANSFERASE / Histone Acetyltransferase / Gcn5-related N-acetyltransferase / inhibitor complex / transcription factor | ||||||
Function / homology | Function and homology information SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Oxidative Stress Induced Senescence / chromatin organization => GO:0006325 / Assembly of the ORC complex at the origin of replication / sexual sporulation resulting in formation of a cellular spore / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / replication fork protection complex ...SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Oxidative Stress Induced Senescence / chromatin organization => GO:0006325 / Assembly of the ORC complex at the origin of replication / sexual sporulation resulting in formation of a cellular spore / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / replication fork protection complex / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / CENP-A containing nucleosome / histone acetyltransferase activity / histone acetyltransferase / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Poux, A.N. / Cebrat, M. / Kim, C.M. / Cole, P.A. / Marmorstein, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Structure of the GCN5 histone acetyltransferase bound to a bisubstrate inhibitor. Authors: Poux, A.N. / Cebrat, M. / Kim, C.M. / Cole, P.A. / Marmorstein, R. | ||||||
History |
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Remark 600 | HETEROGEN INHIBITOR COMPOSED OF A HISTONE H3 FRAGMENT (RESIDUES 1-20) AND A COENZYME A MOLECULE ...HETEROGEN INHIBITOR COMPOSED OF A HISTONE H3 FRAGMENT (RESIDUES 1-20) AND A COENZYME A MOLECULE COVALENTLY BOUND THROUGH AN ISOPROPIONYL LINKER TO LYS14. | ||||||
Remark 999 | SEQUENCE Residue 90 (Chain A) and residue 390 (Chain C) are both PHE. Author indicates that PHE is ...SEQUENCE Residue 90 (Chain A) and residue 390 (Chain C) are both PHE. Author indicates that PHE is present in many of the GCN5 homologues at that position. According to the author, residue 210 (Chain A) and residue 510 (Chain C) are both ARG and not ASN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m1d.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m1d.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/1m1d ftp://data.pdbj.org/pub/pdb/validation_reports/m1/1m1d | HTTPS FTP |
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-Related structure data
Related structure data | 1qsnS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19457.658 Da / Num. of mol.: 2 / Fragment: Catalytic Domain 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: GenBank: 1245146, UniProt: Q27198*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Protein/peptide | Mass: 3011.146 Da / Num. of mol.: 2 Fragment: 20 MER PEPTIDE (RESIDUES 1-20), Bisubstrate analog Source method: obtained synthetically Details: Inhibitor composed of a histone H3 fragment (residues 1-20) is chemically synthesized. The peptide's sequence occurs naturally in Saccharomyces cerevisiae (Baker's yeast). References: UniProt: P02303, UniProt: P61830*PLUS #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.09 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: Ammonium sulfate, sodium cacodylate, sodium chloride, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0082 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 22, 2001 |
Radiation | Monochromator: Rosenbaum-Rock / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0082 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 27647 / Num. obs: 26519 / % possible obs: 96.1 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 97.7 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 37.3 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 97.7 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QSN Resolution: 2.2→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refinement | *PLUS Lowest resolution: 37.3 Å / % reflection Rfree: 10 % / Rfactor all: 0.271 / Rfactor obs: 0.26 / Rfactor Rfree: 0.2652 / Rfactor Rwork: 0.2134 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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