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Open data
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Basic information
Entry | Database: PDB / ID: 6l1i | ||||||
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Title | Crystal Structure Of of PHF20L1 Tudor1 Y24W/Y29W mutant | ||||||
![]() | PHD finger protein 20-like protein 1 | ||||||
![]() | METAL BINDING PROTEIN / PHF20L1 / Tudor / Y24W/Y29W | ||||||
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 | ![]() | 45.1 KB | Display | ![]() |
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PDB format | ![]() | 29.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.2 KB | Display | ![]() |
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Full document | ![]() | 432.2 KB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l0xC ![]() 6l10C ![]() 6l1cC ![]() 6l1fC ![]() 6l1pC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 8739.877 Da / Num. of mol.: 1 / Mutation: Y24W,Y29W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30% PEG 4000, 0.2M Lithium Sulfate, 0.1M Tris, PH 8.0 |
-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: Mar 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.849→27.34 Å / Num. obs: 5374 / % possible obs: 99.52 % / Redundancy: 9.9 % / Biso Wilson estimate: 25.53 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 500 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SD4 Resolution: 1.849→27.333 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 21.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.34 Å2 / Biso mean: 27.2382 Å2 / Biso min: 16.92 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.849→27.333 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 / Origin x: 23.0441 Å / Origin y: 8.3272 Å / Origin z: 0.1 Å
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Refinement TLS group | Selection details: (chain 'B' and resid 3 through 70) |