+Open data
-Basic information
Entry | Database: PDB / ID: 7d8f | |||||||||
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Title | The crystal structure of ScNTM1 in complex with SAH | |||||||||
Components | Alpha N-terminal protein methyltransferase 1 | |||||||||
Keywords | TRANSFERASE / ScNTM1 / N-terminal methylation / methyltransferase / Saccharomyces cerevisiae / substrate binding pocket | |||||||||
Function / homology | Function and homology information N-terminal protein amino acid methylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / methyltransferase activity / cytoplasmic translation / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||
Authors | Zhang, H.Y. / Yue, J. / Zhu, Z.L. | |||||||||
Funding support | China, 2items
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Citation | Journal: Crystallography Reports / Year: 2021 Title: Structural Basis for Peptide Binding of Alpha-N Terminal Methyltransferase from Saccharomyces cerevisiae Authors: Zhang, H.Y. / Kuang, Z. / Xue, L. / Yue, J. / Khan, M.H. / Zhu, Z. / Niu, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d8f.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d8f.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 7d8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/7d8f ftp://data.pdbj.org/pub/pdb/validation_reports/d8/7d8f | HTTPS FTP |
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-Related structure data
Related structure data | 7d8dC 2ex4S 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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Unit cell |
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-Components
#1: Protein | Mass: 26375.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TAE1, NTM1, YBR261C, YBR1729 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P38340, protein N-terminal methyltransferase |
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#2: Chemical | ChemComp-SAH / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.8M sodium acetate trihydrate pH 7.0, 3.5M sodium formate pH 7.0, 20% PEG3350,0.2M magnesium nitrate hexahydrate PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 88586 / % possible obs: 89.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 10.4 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 3.3 % / Num. unique obs: 2039 / CC1/2: 0.559 / % possible all: 42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EX4 Resolution: 1.15→23.91 Å / SU ML: 0.0769 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.3207 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: 14.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→23.91 Å
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Refine LS restraints |
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LS refinement shell |
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