+Open data
-Basic information
Entry | Database: PDB / ID: 7v6p | |||||||||||||||||||||
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Title | Crystal structure of human sNASP TPR domain | |||||||||||||||||||||
Components | Isoform 2 of Nuclear autoantigenic sperm protein | |||||||||||||||||||||
Keywords | CHAPERONE / Histone chaperone | |||||||||||||||||||||
Function / homology | Function and homology information : / chromatin organization => GO:0006325 / CENP-A containing chromatin assembly / DNA replication-dependent chromatin assembly / response to testosterone / blastocyst development / G1/S transition of mitotic cell cycle / nucleosome assembly / male gonad development / protein transport ...: / chromatin organization => GO:0006325 / CENP-A containing chromatin assembly / DNA replication-dependent chromatin assembly / response to testosterone / blastocyst development / G1/S transition of mitotic cell cycle / nucleosome assembly / male gonad development / protein transport / histone binding / DNA replication / chromatin / protein-containing complex binding / protein-containing complex / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | |||||||||||||||||||||
Authors | Liu, C.P. / Xu, R.M. | |||||||||||||||||||||
Funding support | China, 6items
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Citation | Journal: Genes Dev. / Year: 2021 Title: Distinct histone H3-H4 binding modes of sNASP reveal the basis for cooperation and competition of histone chaperones. Authors: Liu, C.P. / Jin, W. / Hu, J. / Wang, M. / Chen, J. / Li, G. / Xu, R.M. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v6p.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v6p.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 7v6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/7v6p ftp://data.pdbj.org/pub/pdb/validation_reports/v6/7v6p | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31924.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NASP / Production host: Escherichia coli (E. coli) / References: UniProt: P49321 | ||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.44 Å3/Da / Density % sol: 72.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium cacodylate, pH 6.5 32% (v/v) PEG 300 0.2 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 13286 / % possible obs: 98.5 % / Redundancy: 8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 31.1 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2280 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→15 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 36.3599 Å / Origin y: 20.6422 Å / Origin z: 85.6868 Å
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Refinement TLS group | Selection details: all |