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Yorodumi- PDB-2dze: Crystal structure of histone chaperone Asf1 in complex with a C-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dze | ||||||
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Title | Crystal structure of histone chaperone Asf1 in complex with a C-terminus of histone H3 | ||||||
Components |
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Keywords | CHAPERONE / Immunoglobulin fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Assembly of the ORC complex at the origin of replication / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / nucleolar peripheral inclusion body / Oxidative Stress Induced Senescence / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / H3-H4 histone complex chaperone activity / RNA Polymerase I Promoter Escape ...Assembly of the ORC complex at the origin of replication / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / nucleolar peripheral inclusion body / Oxidative Stress Induced Senescence / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / H3-H4 histone complex chaperone activity / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / mating-type region heterochromatin / heterochromatin boundary formation / mitotic sister chromatid biorientation / histone chaperone activity / chromosome, subtelomeric region / chromatin-protein adaptor activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / heterochromatin / pericentric heterochromatin / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / histone binding / chromatin remodeling / protein heterodimerization activity / DNA damage response / chromatin / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Padmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of histone chaperone Asf1 in complex with a C-terminus of histone H3 Authors: Padmanabhan, B. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dze.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dze.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/2dze ftp://data.pdbj.org/pub/pdb/validation_reports/dz/2dze | HTTPS FTP |
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-Related structure data
Related structure data | 2cu9S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
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-Components
#1: Protein | Mass: 18347.934 Da / Num. of mol.: 2 / Fragment: N-termianl region, residues 1-162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: cia1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O74515 #2: Protein/peptide | | Mass: 1290.582 Da / Num. of mol.: 1 / Fragment: C-terminal H3 peptide / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P09988 #3: Chemical | #4: 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: 3.02 Å3/Da / Density % sol: 59.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG6000, AS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 41187 / Num. obs: 38738 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.191 / Num. unique all: 3746 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2CU9 Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.63 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20 /
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