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Yorodumi- PDB-8ri0: Crystal structure of Tm1570 domain from Calditerrivibrio nitrored... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ri0 | |||||||||
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Title | Crystal structure of Tm1570 domain from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine | |||||||||
Components | tRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase | |||||||||
Keywords | TRANSFERASE / TrmD-Tm1570 / Tm1570 / Knotted Protein | |||||||||
Function / homology | Function and homology information tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / cytoplasm Similarity search - Function | |||||||||
Biological species | Calditerrivibrio nitroreducens DSM 19672 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Kluza, A. / Lewandowska, I. / Sulkowska, J. | |||||||||
Funding support | Poland, European Union, 2items
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Citation | Journal: To Be Published Title: Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens. To be published Authors: Sulkowska, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ri0.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ri0.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ri0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/8ri0 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/8ri0 | HTTPS FTP |
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-Related structure data
Related structure data | 8b1nC 8byhC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23468.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Calditerrivibrio nitroreducens DSM 19672 (bacteria) Gene: trmD, Calni_2012 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: E4THH1, tRNA (guanine37-N1)-methyltransferase #2: Chemical | #3: 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: 1.94 Å3/Da / Density % sol: 36.77 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: Protein solution: 20 mg/mL Tm1570 in 50 mM HEPES buffer pH 7.4, 300 mM NaCl, 5% glycerol, with addition of 5 mM SAM, 5 mM MgCl2, 0.1% DDM. Reservoir solution: 0.1 M Tris pH 8.5, 20% v/v ethanol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→47.48 Å / Num. obs: 26147 / % possible obs: 98.4 % / Redundancy: 3.31 % / Biso Wilson estimate: 36.82 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.073 / Net I/σ(I): 10.04 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 3.44 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4233 / CC1/2: 0.696 / Rrim(I) all: 0.959 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30.66 Å / SU ML: 0.2781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3311 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→30.66 Å
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Refine LS restraints |
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LS refinement shell |
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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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