+Open data
-Basic information
Entry | Database: PDB / ID: 6l0x | ||||||
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Title | The First Tudor Domain of PHF20L1 | ||||||
Components | PHD finger protein 20-like protein 1 | ||||||
Keywords | METAL BINDING PROTEIN / PHF20L1 / Tudor / apo | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Lv, M.Q. / Gao, J. | ||||||
Citation | Journal: J Phys Chem Lett / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l0x.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l0x.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 6l0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l0x_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
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Full document | 6l0x_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 6l0x_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 6l0x_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/6l0x ftp://data.pdbj.org/pub/pdb/validation_reports/l0/6l0x | HTTPS FTP |
-Related structure data
Related structure data | 6l10C 6l1cC 6l1fC 6l1iC 6l1pC 3sd4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8693.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20L1, CGI-72 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MW92 #2: Chemical | ChemComp-CIT / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 6000, 0.1M citric acid, PH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 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: 1.3→25.32 Å / Num. obs: 29808 / % possible obs: 89.3 % / Redundancy: 3 % / Biso Wilson estimate: 14.06 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.3→1.35 Å / Rmerge(I) obs: 0.363 / Num. unique obs: 1817 / Rsym value: 0.363 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SD4 Resolution: 1.3→25.317 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 20.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.57 Å2 / Biso mean: 19.8837 Å2 / Biso min: 9.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→25.317 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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