+Open data
-Basic information
Entry | Database: PDB / ID: 2xyi | ||||||
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Title | Crystal Structure of Nurf55 in complex with a H4 peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / REPRESSOR / PHOSPHOPROTEIN / WD-REPEAT | ||||||
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 / RCAF complex / eggshell chorion gene amplification / Myb complex ...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 / RCAF complex / 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 / nuclear chromosome / Sin3-type complex / regulation of mitotic cell cycle / heterochromatin formation / nucleosome assembly / structural constituent of chromatin / histone deacetylase binding / nucleosome / chromosome / chromatin organization / histone binding / transcription regulator complex / nucleic acid binding / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / 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 / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Stirnimann, C.U. / Nowak, A.J. / Mueller, C.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Chromatin-Modifying Complex Component Nurf55/P55 Associates with Histones H3, H4 and Polycomb Repressive Complex 2 Subunit Su(Z)12 Through Partially Overlapping Binding Sites. Authors: Nowak, A.J. / Alfieri, C. / Stirnimann, C.U. / Rybin, V. / Baudin, F. / Ly-Hartig, N. / Lindner, D. / Muller, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xyi.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xyi.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/2xyi ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xyi | HTTPS FTP |
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-Related structure data
Related structure data | 3c99S 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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Unit cell |
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-Components
#1: Protein | Mass: 48689.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PFASTBACHT / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q24572 | ||||
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#2: Protein/peptide | Mass: 2253.764 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-46 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P84040 | ||||
#3: Chemical | #4: Chemical | #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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 / Details: 35%(V/V) PEG 400, 100MM MES PH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.0085 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0085 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→25 Å / Num. obs: 46472 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 18.64 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.75→1.85 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.1 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3C99 Resolution: 1.75→24.397 Å / SU ML: 0.05 / σ(F): 1.99 / Phase error: 17.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.22 Å2 / ksol: 0.377 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.272 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→24.397 Å
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Refine LS restraints |
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LS refinement shell |
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