+Open data
-Basic information
Entry | Database: PDB / ID: 7wm5 | ||||||
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Title | Crystal structure of apo TrmM from Mycoplasma capricolum | ||||||
Components | Methyltransferase | ||||||
Keywords | TRANSFERASE / t6A / m6A / methyltransferase | ||||||
Function / homology | Function and homology information : / macromolecule modification / primary metabolic process / S-adenosylmethionine-dependent methyltransferase activity / : / methylation / nucleic acid binding Similarity search - Function | ||||||
Biological species | Mycoplasma capricolum subsp. capricolum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Jeong, H. / Kim, J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Protein Sci. / Year: 2022 Title: Structural and functional characterization of TrmM in m 6 A modification of bacterial tRNA. Authors: Jeong, H. / Lee, Y. / Kim, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wm5.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wm5.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 7wm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/7wm5 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/7wm5 | HTTPS FTP |
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-Related structure data
Related structure data | 7wm6C 3lpmS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30048.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma capricolum subsp. capricolum (bacteria) Gene: MCGM508_01850 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0C2W699 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.0 M Sodium chloride 10% w/v Polyethylene glycol 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→30 Å / Num. obs: 13888 / % possible obs: 93.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 40.09 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.039 / Rrim(I) all: 0.091 / Χ2: 0.805 / Net I/σ(I): 5.8 / Num. measured all: 71295 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LPM Resolution: 2.15→26.51 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.83 / 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: 90.49 Å2 / Biso mean: 49.2221 Å2 / Biso min: 31.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→26.51 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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