+Open data
-Basic information
Entry | Database: PDB / ID: 3c99 | ||||||
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Title | Structural Basis of Histone H4 Recognition by p55 | ||||||
Components | Chromatin assembly factor 1 p55 subunit | ||||||
Keywords | TRANSCRIPTION REPRESSOR / WD40 / histone binding / chromatin / epigenetics / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / WD repeat / NUCLEAR PROTEIN | ||||||
Function / homology | Function and homology information G0 and Early G1 / HDACs deacetylate histones / Regulation of TP53 Activity through Acetylation / Oxidative Stress Induced Senescence / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / eggshell chorion gene amplification / Myb complex / segment specification ...G0 and Early G1 / HDACs deacetylate histones / Regulation of TP53 Activity through Acetylation / Oxidative Stress Induced Senescence / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / eggshell chorion gene amplification / Myb complex / segment specification / CAF-1 complex / polytene chromosome / facultative heterochromatin formation / nucleosome organization / NURF complex / NuRD complex / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / histone methyltransferase complex / Sin3-type complex / heterochromatin formation / regulation of mitotic cell cycle / histone deacetylase binding / chromatin organization / histone binding / transcription regulator complex / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Song, J.J. / Garlick, J.D. / Kingston, R.E. | ||||||
Citation | Journal: Genes Dev. / Year: 2008 Title: Structural basis of histone H4 recognition by p55. Authors: Song, J.J. / Garlick, J.D. / Kingston, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c99.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c99.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 3c99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/3c99 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/3c99 | HTTPS FTP |
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-Related 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: 48817.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Caf1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q24572 |
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#2: Chemical | ChemComp-CD / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.63 Å3/Da / Density % sol: 81.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 9, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 28933 / Num. obs: 28772 / % possible obs: 99.7 % / Redundancy: 14.6 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 44.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / Num. unique all: 576 / Rsym value: 0.55 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: initial model from Se Data Resolution: 2.9→50 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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