+Open data
-Basic information
Entry | Database: PDB / ID: 5bs7 | |||||||||||||||
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Title | Structure of histone H3/H4 in complex with Spt2 | |||||||||||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR / chaperone / transcription | |||||||||||||||
Function / homology | Function and homology information histone chaperone activity / RNA polymerase I core binding / transcription by RNA polymerase I / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / protein heterodimerization activity / regulation of DNA-templated transcription ...histone chaperone activity / RNA polymerase I core binding / transcription by RNA polymerase I / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / protein heterodimerization activity / regulation of DNA-templated transcription / nucleolus / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||
Biological species | Xenopus laevis (African clawed frog) Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||||||||
Authors | Chen, S. / Patel, D.J. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Genes Dev. / Year: 2015 Title: Structure-function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2. Authors: Chen, S. / Rufiange, A. / Huang, H. / Rajashankar, K.R. / Nourani, A. / Patel, D.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bs7.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bs7.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 5bs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bs7_validation.pdf.gz | 479.8 KB | Display | wwPDB validaton report |
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Full document | 5bs7_full_validation.pdf.gz | 486.1 KB | Display | |
Data in XML | 5bs7_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5bs7_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/5bs7 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/5bs7 | HTTPS FTP |
-Related structure data
Related structure data | 5bsaC 1aoiS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12744.906 Da / Num. of mol.: 2 / Fragment: residues 26-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 14351.676 Da / Num. of mol.: 2 / Fragment: residues 571-685 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPTY2D1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68D10 #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.02 M NaCl, 0.2 M HEPES 7.5, 1.5 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→121.2 Å / Num. obs: 13876 / % possible obs: 99 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.1 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AOI Resolution: 3.3→121.2 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.826 / SU B: 20.36 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.533 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.348 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→121.2 Å
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Refine LS restraints |
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