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Open data
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Basic information
Entry | Database: PDB / ID: 6l1p | ||||||
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Title | Crystal structure of PHF20L1 in complex with Hit 1 | ||||||
![]() | PHD finger protein 20-like protein 1 | ||||||
![]() | METAL BINDING PROTEIN / PHF20L1 / Tudor / Hit1 | ||||||
Function / homology | ![]() methylation-dependent protein binding / NSL complex / Formation of WDR5-containing histone-modifying complexes / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein catabolic process / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lv, M.Q. / Gao, J. | ||||||
![]() | ![]() Title: Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1. Authors: Lv, M. / Gao, J. / Li, M. / Ma, R. / Li, F. / Liu, Y. / Liu, M. / Zhang, J. / Yao, X. / Wu, J. / Shi, Y. / Tang, Y. / Pan, Y. / Zhang, Z. / Ruan, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.7 KB | Display | ![]() |
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PDB format | ![]() | 109.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l0xC ![]() 6l10C ![]() 6l1cC ![]() 6l1fC ![]() 6l1iC ![]() 3sd4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8693.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-E3X / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6M magnesium sulfate, 0.1mM MES, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→36.9 Å / Num. obs: 80879 / % possible obs: 100 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 1.23→1.28 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 7.1 / Num. unique obs: 7954 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SD4 Resolution: 1.231→36.899 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 17.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.39 Å2 / Biso mean: 13.488 Å2 / Biso min: 5.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.231→36.899 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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