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Yorodumi- PDB-6zxw: Structure of Archaeoglobus fulgidus Trm11-Trm112 m2G10 tRNA methy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zxw | ||||||
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Title | Structure of Archaeoglobus fulgidus Trm11-Trm112 m2G10 tRNA methyltransferase complex bound to sinefungin | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / tRNA modifications / Epitranscriptomics / Methyltransferase / Heterodimeric enzyme | ||||||
Function / homology | Function and homology information tRNA (guanine10-N2)-dimethyltransferase / tRNA (guanine(10)-N2)-dimethyltransferase activity / tRNA (guanine(10)-N2)-methyltransferase activity / tRNA methylation / tRNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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 | 6zxw.cif.gz | 173.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zxw.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 6zxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/6zxw ftp://data.pdbj.org/pub/pdb/validation_reports/zx/6zxw | HTTPS FTP |
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-Related structure data
Related structure data | 6zxvSC 6zxyC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules GH
#1: Protein | Mass: 37551.301 Da / Num. of mol.: 1 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 |
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#2: Protein | Mass: 6833.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_0284, XD48_0149 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A117KMN5 |
-Non-polymers , 6 types, 80 molecules
#3: Chemical | ChemComp-SFG / | ||||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ZN / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 4 Å3/Da / Density % sol: 69.25 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Sodium citrate pH 6; 9% PEG 4000, 0.1 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→39.55 Å / Num. obs: 36999 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 66.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.19→2.33 Å / Rmerge(I) obs: 1.231 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5852 / CC1/2: 0.522 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZXV Resolution: 2.19→39.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.139
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Displacement parameters | Biso max: 172.57 Å2 / Biso mean: 72.26 Å2 / Biso min: 41.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.19→39.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.21 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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