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Yorodumi- PDB-7bp5: Structural insights into nucleosome reorganization by NAP1-RELATE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bp5 | |||||||||
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Title | Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) | |||||||||
Components |
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Keywords | NUCLEAR PROTEIN / complex / Histone / PLANT PROTEIN | |||||||||
Function / homology | Function and homology information DNA-mediated transformation / histone chaperone activity / positive regulation of neural precursor cell proliferation / positive regulation of neurogenesis / plastid / chloroplast / response to bacterium / nucleosome assembly / response to wounding / structural constituent of chromatin ...DNA-mediated transformation / histone chaperone activity / positive regulation of neural precursor cell proliferation / positive regulation of neurogenesis / plastid / chloroplast / response to bacterium / nucleosome assembly / response to wounding / structural constituent of chromatin / melanosome / nucleosome / nervous system development / histone binding / DNA replication / protein heterodimerization activity / chromatin binding / positive regulation of cell population proliferation / chromatin / nucleolus / DNA binding / RNA binding / extracellular region / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | |||||||||
Authors | Luo, Q. / Baihui, W. | |||||||||
Funding support | China, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: NAP1-Related Protein 1 (NRP1) has multiple interaction modes for chaperoning histones H2A-H2B. Authors: Luo, Q. / Wang, B. / Wu, Z. / Jiang, W. / Wang, Y. / Du, K. / Zhou, N. / Zheng, L. / Gan, J. / Shen, W.H. / Ma, J. / Dong, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bp5.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bp5.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/7bp5 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/7bp5 | 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: 10033.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RAT5, H2A-1, At5g54640, MRB17.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LD28 |
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#2: Protein | Mass: 11033.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g07790, F24B9.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LQQ4 |
#3: Protein/peptide | Mass: 880.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P55209*PLUS |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.18 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium acetate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 38099 / % possible obs: 99.8 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.021 / Rrim(I) all: 0.07 / Χ2: 0.971 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3778 / CC1/2: 0.212 / CC star: 0.592 / Rpim(I) all: 0.214 / Rrim(I) all: 0.548 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→29.94 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.444 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.033 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.3 Å2 / Biso mean: 21.112 Å2 / Biso min: 10.69 Å2
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Refinement step | Cycle: final / Resolution: 1.9→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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