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Yorodumi- PDB-6zxv: Structure of Archaeoglobus fulgidus Trm11 m2G10 tRNA methyltransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zxv | ||||||
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Title | Structure of Archaeoglobus fulgidus Trm11 m2G10 tRNA methyltransferase enzyme bound to sinefungin | ||||||
Components | tRNA (Guanine(10)-N2)-dimethyltransferase | ||||||
Keywords | RNA BINDING PROTEIN / tRNA modifications / Epitranscriptomics / Methyltransferase / Heterodimeric enzyme | ||||||
Function / homology | Function and homology information tRNA (guanine10-N2)-dimethyltransferase / : / tRNA methylation / tRNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å | ||||||
Authors | Graille, M. / Wang, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Functional and structural characterization of the Trm11-Trm112 m2G10 tRNA methyltransferase complex Authors: Wang, C. / Tran, N.V. / Jactel, V. / Guerineau, V. / Graille, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zxv.cif.gz | 275.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zxv.ent.gz | 229.1 KB | Display | PDB format |
PDBx/mmJSON format | 6zxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/6zxv ftp://data.pdbj.org/pub/pdb/validation_reports/zx/6zxv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38932.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_1676, XD48_1558 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A117KU88, UniProt: O29011*PLUS #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Hepes pH 7, 0.8 M KNaTartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980096 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980096 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. obs: 54554 / % possible obs: 98.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.78 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.88→2 Å / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8304 / CC1/2: 0.585 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.88→21.68 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.154
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Displacement parameters | Biso max: 123.32 Å2 / Biso mean: 39.11 Å2 / Biso min: 17.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.88→21.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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