[English] 日本語
Yorodumi- PDB-8h1b: Crystal structure of MnmM from S. aureus complexed with SAM and t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h1b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MnmM from S. aureus complexed with SAM and tRNA anti-codon stem loop (ASL) (1.55 A) | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/RNA / Methyltransferase / tRNA post-transcriptional modification / MnmC mnm5(s2)U / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / tRNA processing / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Kim, J. / Cho, G. / Lee, J. | ||||||
Funding support | Korea, Republic Of, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8h1b.cif.gz | 218.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8h1b.ent.gz | 171.3 KB | Display | PDB format |
PDBx/mmJSON format | 8h1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h1b_validation.pdf.gz | 940.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8h1b_full_validation.pdf.gz | 942.8 KB | Display | |
Data in XML | 8h1b_validation.xml.gz | 22 KB | Display | |
Data in CIF | 8h1b_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/8h1b ftp://data.pdbj.org/pub/pdb/validation_reports/h1/8h1b | HTTPS FTP |
-Related structure data
Related structure data | 8h0sC 8h0tC 8h1aC 8h27C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21964.928 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_01878 / Plasmid: pLATE31 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q2FXG9, Transferases; Transferring one-carbon groups; Methyltransferases #2: RNA chain | Mass: 5380.221 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→47.12 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.552→1.593 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|