+Open data
-Basic information
Entry | Database: PDB / ID: 2z34 | ||||||
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Title | Crystal structure of SpCia1/Asf1 complex with Hip1 | ||||||
Components |
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Keywords | CHAPERONE / histone chaperone / nucleosome disassmebly/assembly / chromatin regulation / Chromatin regulator / Coiled coil / Nucleus / Transcription / Transcription regulation / Cytoplasm / Repressor / WD repeat / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information : / chromatin organization => GO:0006325 / HIR complex / H3-H4 histone complex chaperone activity / histone chaperone activity / chromatin => GO:0000785 / nucleosome organization / DNA replication-dependent chromatin assembly / nucleosome disassembly / mitotic sister chromatid segregation ...: / chromatin organization => GO:0006325 / HIR complex / H3-H4 histone complex chaperone activity / histone chaperone activity / chromatin => GO:0000785 / nucleosome organization / DNA replication-dependent chromatin assembly / nucleosome disassembly / mitotic sister chromatid segregation / transcription corepressor activity / nucleosome assembly / chromatin organization / histone binding / chromatin remodeling / DNA-templated transcription / chromatin / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Malay, A.D. / Padmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal structures of fission yeast histone chaperone Asf1 complexed with the Hip1 B-domain or the Cac2 C terminus Authors: Malay, A.D. / Umehara, T. / Matsubara-Malay, K. / 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 | 2z34.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z34.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 2z34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z34_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 2z34_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 2z34_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 2z34_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/2z34 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/2z34 | HTTPS FTP |
-Related structure data
Related structure data | 2cu9SC 2z3fC 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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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
#1: Protein | Mass: 18347.934 Da / Num. of mol.: 2 / Fragment: N-terminal region 1-161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: cia1, asf1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O74515 #2: Protein/peptide | Mass: 3202.869 Da / Num. of mol.: 2 / Fragment: Hip1 B domain peptide / Source method: obtained synthetically Details: Synthetic peptide: The sequence corresponding to 469-497 in HIR1_SCHPO References: UniProt: P87314 #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: 2.16 Å3/Da / Density % sol: 43.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25% PEG3350, 0.18M Ammonium Fluoride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 15, 2006 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 16590 / Num. obs: 16188 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.237 / Num. unique all: 1621 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CU9 Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.425 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.59 / ESU R Free: 0.29 / 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: 29.602 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20 /
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