+Open data
-Basic information
Entry | Database: PDB / ID: 7f4r | ||||||
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Title | Crystal structure of MTA1 | ||||||
Components | MT-a70 family protein | ||||||
Keywords | DNA BINDING PROTEIN / Protein Complex | ||||||
Function / homology | MT-A70-like / MT-A70 / MT-A70-like family profile. / RNA N6-methyladenosine methyltransferase complex / methyltransferase activity / S-adenosyl-L-methionine-dependent methyltransferase superfamily / nucleus / MT-a70 family protein Function and homology information | ||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Chen, J. / Liu, L. | ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for MTA1c-mediated DNA N6-adenine methylation Authors: Chen, J. / Hu, R. / Chen, Y. / Lin, X. / Xiang, W. / Chen, H. / Yao, C. / Liu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f4r.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f4r.ent.gz | 129.5 KB | Display | PDB format |
PDBx/mmJSON format | 7f4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f4r_validation.pdf.gz | 463.7 KB | Display | wwPDB validaton report |
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Full document | 7f4r_full_validation.pdf.gz | 489.4 KB | Display | |
Data in XML | 7f4r_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 7f4r_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/7f4r ftp://data.pdbj.org/pub/pdb/validation_reports/f4/7f4r | HTTPS FTP |
-Related structure data
Related structure data | 7f4lC 7f4mC 7f4nC 7f4oSC 7f4pC 7f4qC 7f4sC 7f4tC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 23113.408 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila (strain SB210) (eukaryote) Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q22GC0 #2: Water | ChemComp-HOH / | |
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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: 2.22 Å3/Da / Density % sol: 44.66 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.15M potassium sodium tartrate, 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→50 Å / Num. obs: 54422 / % possible obs: 92.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 18.39 Å2 / Rpim(I) all: 0.049 / Net I/σ(I): 11.79 |
Reflection shell | Resolution: 1.83→1.86 Å / Mean I/σ(I) obs: 1.43 / Num. unique obs: 3299 / Rpim(I) all: 0.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7F4O Resolution: 1.83→28.73 Å / SU ML: 0.2199 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.4044 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: 26.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→28.73 Å
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Refine LS restraints |
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LS refinement shell |
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