+Open data
-Basic information
Entry | Database: PDB / ID: 7mjy | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | MiaB in the complex with s-adenosyl-L-homocysteine and RNA | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSFERASE/RNA / tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase / TRANSFERASE / TRANSFERASE-RNA complex | ||||||||||||
Function / homology | Function and homology information tRNA methylthiolation / tRNA-2-methylthio-N6-dimethylallyladenosine synthase / methylthiotransferase activity / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Bacteroides uniformis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||||||||
Authors | Esakova, O.A. / Grove, T.L. / Yennawar, N.H. / Arcinas, A.J. / Wang, B. / Krebs, C. / Almo, S.C. / Booker, S.J. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Nature / Year: 2021 Title: Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB. Authors: Esakova, O.A. / Grove, T.L. / Yennawar, N.H. / Arcinas, A.J. / Wang, B. / Krebs, C. / Almo, S.C. / Booker, S.J. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7mjy.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7mjy.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 7mjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mjy_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7mjy_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7mjy_validation.xml.gz | 21 KB | Display | |
Data in CIF | 7mjy_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/7mjy ftp://data.pdbj.org/pub/pdb/validation_reports/mj/7mjy | HTTPS FTP |
-Related structure data
Related structure data | 7mjvC 7mjwC 7mjxC 7mjzC 2qgqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / RNA chain , 2 types, 2 molecules AM
#1: Protein | Mass: 51275.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis (bacteria) Gene: miaB_2, miaB, DW795_02470, DW831_10175, DWW14_18715, DWX44_14905, DXC07_08890, DXC80_15965, DXD90_15595, ERS417307_03809, GAP41_19630, GAP48_15545, GAP55_16410, GAQ44_15640 Production host: Escherichia coli (E. coli) References: UniProt: A0A174NUT3, tRNA-2-methylthio-N6-dimethylallyladenosine synthase |
---|---|
#2: RNA chain | Mass: 4141.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacteroides uniformis (bacteria) |
-Non-polymers , 7 types, 200 molecules
#3: Chemical | #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-F3S / | #6: Chemical | ChemComp-SF4 / | #7: Chemical | ChemComp-SAH / | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.48 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium cacodylate, pH 5.5, 13% PEG 4000, and 3% 1,6-hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0033 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0033 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.86→50 Å / Num. obs: 40640 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 19.33 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.058 / Rrim(I) all: 0.163 / Χ2: 1.048 / Net I/σ(I): 4.8 / Num. measured all: 303282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QGQ Resolution: 1.86→48.37 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.42 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.85 Å2 / Biso mean: 27.1878 Å2 / Biso min: 7.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.86→48.37 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|