+Open data
-Basic information
Entry | Database: PDB / ID: 2z3f | ||||||
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Title | Crystal structure of spCia1/Asf1 complexed with Cac2 peptide | ||||||
Components |
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Keywords | CHAPERONE / Histone chaperone / nucleosome diassembly/assembly / chromatin regulation / Chromatin regulator / Coiled coil / Nucleus / Transcription / Transcription regulation / 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 H3-H4 histone complex chaperone activity / mitotic recombination-dependent replication fork processing / CAF-1 complex / histone chaperone activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / nuclear replication fork / nucleosome assembly / chromatin organization / histone binding ...H3-H4 histone complex chaperone activity / mitotic recombination-dependent replication fork processing / CAF-1 complex / histone chaperone activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / nuclear replication fork / nucleosome assembly / chromatin organization / histone binding / chromatin remodeling / chromatin / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 2z3f.cif.gz | 284.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z3f.ent.gz | 232.2 KB | Display | PDB format |
PDBx/mmJSON format | 2z3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z3f_validation.pdf.gz | 539.5 KB | Display | wwPDB validaton report |
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Full document | 2z3f_full_validation.pdf.gz | 553.7 KB | Display | |
Data in XML | 2z3f_validation.xml.gz | 50.7 KB | Display | |
Data in CIF | 2z3f_validation.cif.gz | 71 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/2z3f ftp://data.pdbj.org/pub/pdb/validation_reports/z3/2z3f | HTTPS FTP |
-Related structure data
Related structure data | 2cu9SC 2z34C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 1 / Auth seq-ID: 3 - 159 / Label seq-ID: 3 - 159
NCS ensembles :
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-Components
#1: Protein | Mass: 18347.934 Da / Num. of mol.: 8 / Fragment: Cia1/Asf1 N-terminal domain, residues 1-162 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: 2276.719 Da / Num. of mol.: 11 / Fragment: cac2 C-terminal domain, residues 493-512 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13985 #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: 2.41 Å3/Da / Density % sol: 48.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.8M Na/K phosphate pH 8.0, 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: Sep 1, 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: 2.6→50 Å / Num. all: 50157 / Num. obs: 50092 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.48 / Num. unique all: 5054 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CU9 Resolution: 2.7→31.6 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.854 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / 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: 38.992 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→31.6 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20 /
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