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- PDB-8h1b: Crystal structure of MnmM from S. aureus complexed with SAM and t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h1b | ||||||
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Title | Crystal structure of MnmM from S. aureus complexed with SAM and tRNA anti-codon stem loop (ASL) (1.55 A) | ||||||
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![]() | TRANSFERASE/RNA / ![]() | ||||||
Function / homology | ![]() tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / tRNA processing / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, J. / Cho, G. / Lee, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.4 KB | Display | ![]() |
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PDB format | ![]() | 171.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8h0sC ![]() 8h0tC ![]() 8h1aC ![]() 8h27C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21964.928 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_01878 / Plasmid: pLATE31 / Production host: ![]() ![]() ![]() References: UniProt: Q2FXG9, ![]() #2: RNA chain | Mass: 5380.221 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-NA / | #5: 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: 2.47 Å3/Da / Density % sol: 50.21 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 20% w/v PEG8000 |
-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: Apr 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.55→47.12 Å / Num. obs: 65003 / % possible obs: 84.6 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.035 / Rrim(I) all: 0.095 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.55→1.66 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.421 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4063 / CC1/2: 0.537 / Rpim(I) all: 0.566 / Rrim(I) all: 1.531 / % possible all: 29.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: AlphaFold model (UniProt: Q2FXG9) Resolution: 1.55→47.12 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.908 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 / 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: 29.176 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→47.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.552→1.593 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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