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Yorodumi- PDB-6ems: Crystal Structure of dual specific Trm10 construct from Thermococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ems | ||||||
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Title | Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis. | ||||||
Components | tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase | ||||||
Keywords | RNA BINDING PROTEIN / Trm10 / Dual specificity enzymes / SPOUT / MTases | ||||||
Function / homology | Function and homology information tRNA (adenine9-N1)-methyltransferase / tRNA (adenine(9)-N1)-methyltransferase activity / tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA methylation / tRNA processing / cytoplasm Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 Å | ||||||
Authors | Singh, R.K. / Versees, W. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: RNA / Year: 2018 Title: Structural and biochemical analysis of the dual-specificity Trm10 enzyme fromThermococcus kodakaraensisprompts reconsideration of its catalytic mechanism. Authors: Singh, R.K. / Feller, A. / Roovers, M. / Van Elder, D. / Wauters, L. / Droogmans, L. / Versees, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ems.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ems.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ems.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/6ems ftp://data.pdbj.org/pub/pdb/validation_reports/em/6ems | HTTPS FTP |
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-Related structure data
Related structure data | 6emtC 6emuC 6emvC 5a7yS 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
#1: Protein | Mass: 42217.750 Da / Num. of mol.: 1 / Mutation: C77A, C120A Source method: isolated from a genetically manipulated source Details: This is a c-terminal deletion construct of the protein Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Gene: TK0422 / Plasmid: Pet28b Details (production host): bacterial expression vector with T7lac promoter Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: Q5JD38, tRNA (adenine9-N1)-methyltransferase, tRNA (guanine9-N1)-methyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 18% PEG3350 and 0.1M Tris pH 7.5 / PH range: 7-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.996→47.0066469139 Å / Num. obs: 20375 / % possible obs: 99.97 % / Redundancy: 19.9 % / Biso Wilson estimate: 49.0376106091 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07567 / Rpim(I) all: 0.0174 / Rrim(I) all: 0.0777 / Net I/σ(I): 24.82 |
Reflection shell | Resolution: 1.996→2.067 Å / Redundancy: 20.1 % / Rmerge(I) obs: 2.289 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1976 / CC1/2: 0.821 / Rpim(I) all: 0.5138 / Rrim(I) all: 2.348 / % possible all: 99.85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5a7y Resolution: 1.996→47.007 Å / SU ML: 0.26777404931 / Cross valid method: THROUGHOUT / σ(F): 1.327 / Phase error: 26.4225135098
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.6575465554 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.996→47.007 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 25.6911600187 Å / Origin y: 37.1920787861 Å / Origin z: 34.5003053449 Å
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Refinement TLS group | Selection details: all |