[English] 日本語
Yorodumi- PDB-7f8c: Crystal structure of rRNA methyltransferase Erm38 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f8c | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of rRNA methyltransferase Erm38 in complex with sinefungin | ||||||
Components | Erm(38) | ||||||
Keywords | TRANSFERASE / erythromycin resistance methyltransferase / methyltransferase / sinefungin | ||||||
Function / homology | Function and homology information rRNA (adenine-N6,N6-)-dimethyltransferase activity / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å | ||||||
Authors | Goh, B.C. / Lescar, J. | ||||||
Funding support | Singapore, 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Crystal structure and functional analysis of mycobacterial erythromycin resistance methyltransferase Erm38 reveals its RNA-binding site. Authors: Goh, B.C. / Xiang, X. / Lescar, J. / Dedon, P.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7f8c.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7f8c.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 7f8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f8c_validation.pdf.gz | 763.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7f8c_full_validation.pdf.gz | 763.9 KB | Display | |
Data in XML | 7f8c_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 7f8c_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/7f8c ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f8c | HTTPS FTP |
-Related structure data
Related structure data | 7f8aSC 7f8bC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28923.498 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: erm(38) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q79N53 |
---|---|
#2: Chemical | ChemComp-SFG / |
#3: Chemical | ChemComp-SIN / |
#4: 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: 2.67 Å3/Da / Density % sol: 53.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0 M succinic acid pH 7, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.248→48.47 Å / Num. obs: 15503 / % possible obs: 99.8 % / Redundancy: 25.9 % / Biso Wilson estimate: 48.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.016 / Rrim(I) all: 0.08 / Net I/σ(I): 31.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7F8A Resolution: 2.248→48.47 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.279 / SU Rfree Blow DPI: 0.217 / SU Rfree Cruickshank DPI: 0.211
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.44 Å2 / Biso mean: 43.25 Å2 / Biso min: 26.27 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.248→48.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 39
|