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Yorodumi- PDB-4nq0: Structural insights into yeast histone chaperone Hif1: a scaffold... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nq0 | ||||||
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Title | Structural insights into yeast histone chaperone Hif1: a scaffold protein recruiting protein complexes to core histones | ||||||
Components | HAT1-interacting factor 1 | ||||||
Keywords | CHAPERONE / TPR / NASP homologue / SHNi-TPR / mediating protein-protein interactions / histone chaperone / Nucleus | ||||||
Function / homology | Function and homology information subtelomeric heterochromatin formation / histone acetyltransferase complex / nucleosome assembly / histone binding / chromosome, telomeric region / protein homodimerization activity / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Liu, H. / Zhang, M. / He, W. / Zhu, Z. / Teng, M. / Gao, Y. / Niu, L. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: Structural insights into yeast histone chaperone Hif1: a scaffold protein recruiting protein complexes to core histones Authors: Liu, H. / Zhang, M. / He, W. / Zhu, Z. / Teng, M. / Gao, Y. / Niu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nq0.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nq0.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 4nq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/4nq0 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/4nq0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44553.188 Da / Num. of mol.: 1 / Fragment: HAT1-interacting factor 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: HIF1, YLL022C, L1205 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12373 |
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#2: 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: 1.75 Å3/Da / Density % sol: 29.9 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M sodium cacodylate, 15% PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 18938 / Num. obs: 18861 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.083 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.1 / Num. unique all: 917 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→41.3 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.71 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.214 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.268 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→41.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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