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Yorodumi- PDB-7twm: Structure of a borosin methyltransferase from Mycena rosella with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7twm | ||||||
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Title | Structure of a borosin methyltransferase from Mycena rosella with peptide CspL(MroMCspL) in complex with SAH | ||||||
Components | MroMCspL | ||||||
Keywords | TRANSFERASE / RIPPs / methyltransferase / borosin / MroMA | ||||||
Function / homology | S-ADENOSYL-L-HOMOCYSTEINE Function and homology information | ||||||
Biological species | Mycena rosella (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Zheng, Y. / Ongpipattanakul, C. / Nair, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Bioconjugate Platform for Iterative Backbone N -Methylation of Peptides. Authors: Zheng, Y. / Ongpipattanakul, C. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7twm.cif.gz | 318.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7twm.ent.gz | 256.5 KB | Display | PDB format |
PDBx/mmJSON format | 7twm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/7twm ftp://data.pdbj.org/pub/pdb/validation_reports/tw/7twm | HTTPS FTP |
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-Related structure data
Related structure data | 7twkSC 7twlC 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: 43996.301 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycena rosella (fungus) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-SAH / #3: 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: 2.82 Å3/Da / Density % sol: 56.33 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 4000, and 100 mM sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→82.7 Å / Num. obs: 145206 / % possible obs: 99.5 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.93→1.94 Å / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1457 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7TWK Resolution: 1.93→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.071 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.99 Å2 / Biso mean: 34.743 Å2 / Biso min: 15.53 Å2
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Refinement step | Cycle: final / Resolution: 1.93→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.932→1.982 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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