+Open data
-Basic information
Entry | Database: PDB / ID: 7f4o | ||||||
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Title | Crystal structure of MTA1-p2 complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA / Protein / Complex | ||||||
Function / homology | Function and homology information RNA N6-methyladenosine methyltransferase complex / methyltransferase activity / membrane / nucleus Similarity search - Function | ||||||
Biological species | Tetrahymena thermophila SB210 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å | ||||||
Authors | Chen, J. / Liu, L. | ||||||
Funding support | China, 1items
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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 | 7f4o.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f4o.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 7f4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f4o_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 7f4o_full_validation.pdf.gz | 478.8 KB | Display | |
Data in XML | 7f4o_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 7f4o_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/7f4o ftp://data.pdbj.org/pub/pdb/validation_reports/f4/7f4o | HTTPS FTP |
-Related structure data
Related structure data | 7f4lC 7f4mC 7f4nC 7f4pC 7f4qC 7f4rC 7f4sC 7f4tC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16612.893 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote) Gene: p2 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: I7M8B9 |
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#2: Protein | Mass: 28809.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote) Gene: MTA1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q22GC0 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 70.45 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, pH 6.5, 15% PEG 550 MME |
-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: Dec 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 12112 / % possible obs: 100 % / Redundancy: 33.2 % / Biso Wilson estimate: 51.44 Å2 / Rpim(I) all: 0.024 / Net I/σ(I): 37.5 |
Reflection shell | Resolution: 3.1→3.15 Å / Mean I/σ(I) obs: 4 / Num. unique obs: 607 / Rpim(I) all: 0.182 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.1→44.98 Å / SU ML: 0.4589 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 26.3898 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: 49.89 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→44.98 Å
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Refine LS restraints |
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LS refinement shell |
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