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- PDB-8h26: Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A) -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h26 | ||||||
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Title | Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A) | ||||||
![]() | 16S rRNA (Cytosine(1402)-N(4))-methyltransferase | ||||||
![]() | TRANSFERASE / Methyltrnasferase tRNA post-transcriptional modification MnmC mnm5(s2)U | ||||||
Function / homology | tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / Putative rRNA methylase / Putative rRNA methylase / tRNA processing / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (mnm(5)s(2)U34)-methyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, J. / Cho, G. / Lee, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A) Authors: Kim, J. / Cho, G. / Lee, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 440.6 KB | Display | ![]() |
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PDB format | ![]() | 363.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 45.5 KB | Display | |
Data in CIF | ![]() | 65.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21964.928 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_01878 / Plasmid: pLATE31 / Production host: ![]() ![]() #2: Chemical | ChemComp-SAH / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 6.5 and 25% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→67.09 Å / Num. obs: 104221 / % possible obs: 92.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.5→1.68 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.285 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5203 / CC1/2: 0.637 / Rpim(I) all: 0.507 / Rrim(I) all: 1.382 / % possible all: 72.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AlphaFold model (UniProt: Q2FXG9) Resolution: 1.5→67.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.95 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.373 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→67.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.541 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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