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Yorodumi- PDB-8h0t: Crystal structure of MnmM from B. subtilis complexed with SAH (1.17 A) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h0t | ||||||
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Title | Crystal structure of MnmM from B. subtilis complexed with SAH (1.17 A) | ||||||
Components | Putative rRNA methylase YtqB | ||||||
Keywords | TRANSFERASE / Methyltransferase / tRNA post-transcriptional modification / MnmC mnm5(s2)U | ||||||
Function / homology | Putative rRNA methylase / Putative rRNA methylase / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Putative rRNA methylase YtqB Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å | ||||||
Authors | Kim, J. / Lee, J. / Cho, G. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification. Authors: Cho, G. / Lee, J. / Kim, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h0t.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h0t.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 8h0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h0t_validation.pdf.gz | 691.7 KB | Display | wwPDB validaton report |
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Full document | 8h0t_full_validation.pdf.gz | 691.6 KB | Display | |
Data in XML | 8h0t_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 8h0t_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/8h0t ftp://data.pdbj.org/pub/pdb/validation_reports/h0/8h0t | HTTPS FTP |
-Related structure data
Related structure data | 8h0sC 8h1aC 8h1bC 8h27C 4ponS 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: 22253.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 / Gene: ytqB, BSU30490 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O34614, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Chemical | ChemComp-SAH / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 25% w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→37.59 Å / Num. obs: 41988 / % possible obs: 72.5 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.16→1.3 Å / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2103 / CC1/2: 0.626 / Rpim(I) all: 0.493 / Rrim(I) all: 0.951 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4PON Resolution: 1.17→37.59 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 14.069 Å2
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Refinement step | Cycle: 1 / Resolution: 1.17→37.59 Å
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Refine LS restraints |
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