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- PDB-5y5w: Crystal structure of human Spindlin1 in complex with a histone H4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5y5w | ||||||
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Title | Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide | ||||||
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Function / homology | ![]() gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, C. / Zang, J. | ||||||
![]() | ![]() Title: Spindlin-1 recognizes methylations of K20 and R23 of histone H4 tail Authors: Wang, C. / Zhan, L. / Wu, M. / Ma, R. / Yao, J. / Xiong, Y. / Pan, Y. / Guan, S. / Zhang, X. / Zang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.7 KB | Display | ![]() |
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PDB format | ![]() | 169.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ns2S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26886.117 Da / Num. of mol.: 4 / Fragment: UNP residues 51-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1212.469 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.79 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.5 M (NH4)2SO4, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.3→84.61 Å / Num. obs: 17175 / % possible obs: 99 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 10.2 / Num. unique obs: 822 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2NS2 Resolution: 3.3→84.61 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.822 / SU B: 70.425 / SU ML: 0.527 / Cross valid method: THROUGHOUT / ESU R Free: 0.648 / 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: 64.962 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→84.61 Å
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Refine LS restraints |
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