+Open data
-Basic information
Entry | Database: PDB / ID: 7vkk | ||||||
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Title | Crystal structure of D. melanogaster SAMTOR V66W/E67P mutant | ||||||
Components | S-adenosylmethionine sensor upstream of mTORC1 | ||||||
Keywords | TRANSFERASE / SAMTOR / SAM | ||||||
Function / homology | S-adenosylmethionine-dependent methyltransferase Bmt2-like / 25S rRNA (adenine(2142)-N(1))-methyltransferase, Bmt2 / S-adenosyl-L-methionine binding / negative regulation of TORC1 signaling / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-adenosylmethionine sensor upstream of mTORC1 Function and homology information | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å | ||||||
Authors | Zhang, T. / Ding, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Molecular mechanism of S -adenosylmethionine sensing by SAMTOR in mTORC1 signaling. Authors: Tang, X. / Zhang, Y. / Wang, G. / Zhang, C. / Wang, F. / Shi, J. / Zhang, T. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vkk.cif.gz | 208.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vkk.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vkk_validation.pdf.gz | 478.2 KB | Display | wwPDB validaton report |
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Full document | 7vkk_full_validation.pdf.gz | 485.5 KB | Display | |
Data in XML | 7vkk_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 7vkk_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/7vkk ftp://data.pdbj.org/pub/pdb/validation_reports/vk/7vkk | HTTPS FTP |
-Related structure data
Related structure data | 7vkqC 7vkrSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35067.242 Da / Num. of mol.: 2 / Fragment: trasnferase / Mutation: V66W, E67P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Samtor, CG3570 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9W138, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-TRS / | #3: Chemical | ChemComp-SO4 / 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: 2.84 Å3/Da / Density % sol: 56.72 % |
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Crystal grow | Temperature: 290 K / Method: evaporation / pH: 5 Details: 1.8 M Ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, and 2% (v/v) PEG monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.55→37.68 Å / Num. obs: 9792 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.168 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.55→3.68 Å / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 950 / CC1/2: 0.686 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VKR Resolution: 3.55→37.68 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.894 / SU B: 75.369 / SU ML: 0.511 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.643 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.71 Å2 / Biso mean: 84.687 Å2 / Biso min: 61.74 Å2
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Refinement step | Cycle: final / Resolution: 3.55→37.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.55→3.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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