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Yorodumi- PDB-7yf3: Crystal structure of METTL9 in complex with unmethylated S100A9 p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yf3 | ||||||
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Title | Crystal structure of METTL9 in complex with unmethylated S100A9 peptide and SAH | ||||||
Components |
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Keywords | TRANSFERASE / METTL9 / S100A9 / histidine methyltransferase | ||||||
Function / homology | Function and homology information protein-L-histidine N-pros-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / endoplasmic reticulum / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.434 Å | ||||||
Authors | Xie, H. / Wang, X. / Xu, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2023 Title: Molecular basis for METTL9-mediated N1-histidine methylation. Authors: Wang, X. / Xie, H. / Guo, Q. / Cao, D. / Ru, W. / Zhao, S. / Zhu, Z. / Zhang, J. / Pan, W. / Yao, X. / Xu, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yf3.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yf3.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 7yf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yf3_validation.pdf.gz | 931.9 KB | Display | wwPDB validaton report |
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Full document | 7yf3_full_validation.pdf.gz | 938.9 KB | Display | |
Data in XML | 7yf3_validation.xml.gz | 21 KB | Display | |
Data in CIF | 7yf3_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/7yf3 ftp://data.pdbj.org/pub/pdb/validation_reports/yf/7yf3 | HTTPS FTP |
-Related structure data
Related structure data | 7y9cC 7yf2SC 7yf4C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31554.012 Da / Num. of mol.: 2 / Mutation: L95A, F96A, L99A, F103A, V107A, F111A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL9, DREV, CGI-81 / Production host: Escherichia coli (E. coli) References: UniProt: Q9H1A3, Transferases; Transferring one-carbon groups; Methyltransferases #2: Protein/peptide | Mass: 1121.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) #3: Chemical | Has ligand of interest | Y | |
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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: 2.09 Å3/Da / Density % sol: 41.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8.5, 0.2 M MgCl2, 30% (w/v) PEG 4000, 0.1 M NDSB-256 |
-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 PILATUS 6M / Detector: PIXEL / Date: Dec 10, 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: 3.43→70.32 Å / Num. obs: 7067 / % possible obs: 94.7 % / Redundancy: 6.3 % / CC1/2: 0.984 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.43→3.64 Å / Num. unique obs: 7067 / CC1/2: 0.797 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YF2 Resolution: 3.434→70.319 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.3 / Stereochemistry target values: ML
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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 max: 85.48 Å2 / Biso mean: 60.1084 Å2 / Biso min: 47.27 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.434→70.319 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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