+Open data
-Basic information
Entry | Database: PDB / ID: 6zd4 | |||||||||
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Title | Crystal structure of YTHDC1 S378A mutant | |||||||||
Components | YTH domain containing 1 | |||||||||
Keywords | RNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Bedi, R.K. / Li, Y. / Caflisch, A. | |||||||||
Funding support | Switzerland, Sweden, 2items
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Citation | Journal: J Chem Theory Comput / Year: 2021 Title: Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m 6 A) Recognition by the Reader Domain of YTHDC1. Authors: Li, Y. / Bedi, R.K. / Wiedmer, L. / Sun, X. / Huang, D. / Caflisch, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zd4.cif.gz | 104 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zd4.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 6zd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/6zd4 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/6zd4 | HTTPS FTP |
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-Related structure data
Related structure data | 6ynnC 6ynoC 6zcmC 6zcnC 6zd3C 6zd5C 6zd7C 6zd8C 6zd9C 6zdaC 4r3hS 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: 20951.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1 / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-SO4 / #3: 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: 1.97 Å3/Da / Density % sol: 37.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 25% PEG3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→40.45 Å / Num. obs: 61908 / % possible obs: 97.4 % / Redundancy: 4.42 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.63 |
Reflection shell | Resolution: 1.4→1.49 Å / Num. unique obs: 9997 / CC1/2: 0.728 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4r3h Resolution: 1.4→40.45 Å / SU ML: 0.2007 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.6885 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→40.45 Å
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Refine LS restraints |
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LS refinement shell |
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