+Open data
-Basic information
Entry | Database: PDB / ID: 7wdq | ||||||
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Title | DsyB in complex with SAM | ||||||
Components | SAM-dependent MTHB methyltransferase | ||||||
Keywords | TRANSFERASE / Complex / SAM-dependent methyltransferase | ||||||
Function / homology | S-ADENOSYLMETHIONINE Function and homology information | ||||||
Biological species | Nisaea denitrificans DSM 18348 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Li, C.Y. | ||||||
Funding support | 1items
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Citation | Journal: Mlife / Year: 2022 Title: Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB. Authors: Li, C.Y. / Crack, J.C. / Newton-Payne, S. / Murphy, A.R.J. / Chen, X.L. / Pinchbeck, B.J. / Zhou, S. / Williams, B.T. / Peng, M. / Zhang, X.H. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wdq.cif.gz | 256.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wdq.ent.gz | 208.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/7wdq ftp://data.pdbj.org/pub/pdb/validation_reports/wd/7wdq | HTTPS FTP |
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-Related structure data
Related structure data | 7wdwC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36185.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nisaea denitrificans DSM 18348 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M NaCl, 0.1 M Hepes (pH 7.5) and 25% (wt/vol) polyethylene glycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→50 Å / Num. obs: 56091 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.45 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Χ2: 3.243 / Net I/σ(I): 15.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→31.94 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.893 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.06 Å2 / Biso mean: 46.9 Å2 / Biso min: 19.8 Å2
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Refinement step | Cycle: final / Resolution: 2.35→31.94 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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