+Open data
-Basic information
Entry | Database: PDB / ID: 7vvw | |||||||||||||||||||||
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Title | MmtN-SAM complex | |||||||||||||||||||||
Components | SAM-dependent methyltransferase | |||||||||||||||||||||
Keywords | TRANSFERASE / SAM-dependent / methyltransferase / rossmann-like / methionine methyltransferase | |||||||||||||||||||||
Function / homology | methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / PHOSPHATE ION / S-ADENOSYLMETHIONINE / SAM-dependent methyltransferase Function and homology information | |||||||||||||||||||||
Biological species | Roseovarius indicus (bacteria) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å | |||||||||||||||||||||
Authors | Zhang, Y.Z. / Peng, M. / Li, C.Y. | |||||||||||||||||||||
Funding support | China, 6items
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Citation | Journal: Nat Commun / Year: 2022 Title: Insights into methionine S-methylation in diverse organisms. Authors: Peng, M. / Li, C.Y. / Chen, X.L. / Williams, B.T. / Li, K. / Gao, Y.N. / Wang, P. / Wang, N. / Gao, C. / Zhang, S. / Schoelmerich, M.C. / Banfield, J.F. / Miller, J.B. / Le Brun, N.E. / Todd, J.D. / Zhang, Y.Z. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vvw.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vvw.ent.gz | 138 KB | Display | PDB format |
PDBx/mmJSON format | 7vvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vvw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7vvw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7vvw_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 7vvw_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/7vvw ftp://data.pdbj.org/pub/pdb/validation_reports/vv/7vvw | HTTPS FTP |
-Related structure data
Related structure data | 7vvvC 7vvxC 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: 32915.488 Da / Num. of mol.: 3 / Mutation: K141A/K143A/K146A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Roseovarius indicus (bacteria) / Gene: XM52_07085 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T5PCK9 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | 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: 2.73 Å3/Da / Density % sol: 54.87 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.2M sodium acetate trihydrate, 0.1M sodium cacodylate trihydrate pH 6.5, 15% (wt/vol) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→93.13 Å / Num. obs: 61893 / % possible obs: 98.63 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.034 / Rrim(I) all: 0.119 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.11→2.19 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6159 / CC1/2: 0.911 / Rpim(I) all: 0.337 / Rrim(I) all: 1.252 / % possible all: 99.94 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.11→93.13 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.51 / 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: 109.05 Å2 / Biso mean: 51.6303 Å2 / Biso min: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.11→93.13 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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