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Yorodumi- PDB-5axn: Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5axn | ||||||
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Title | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP | ||||||
Components |
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Keywords | Transferase/RNA / Transferase / Transferase-RNA complex | ||||||
Function / homology | Function and homology information tRNA guanylyltransferase activity / tRNA modification / GTP binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Methanosarcina acetivorans (archaea) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å | ||||||
Authors | Kimura, S. / Suzuki, T. / Yu, J. / Kato, K. / Yao, M. | ||||||
Citation | Journal: Sci Adv / Year: 2016 Title: Template-dependent nucleotide addition in the reverse (3'-5') direction by Thg1-like protein Authors: Kimura, S. / Suzuki, T. / Chen, M. / Kato, K. / Yu, J. / Nakamura, A. / Tanaka, I. / Yao, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5axn.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5axn.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 5axn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5axn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5axn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5axn_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 5axn_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/5axn ftp://data.pdbj.org/pub/pdb/validation_reports/ax/5axn | HTTPS FTP |
-Related structure data
Related structure data | 5axkC 5axlC 5axmC 1ehzS 3wbzS C: citing same article (ref.) S: Starting model for refinement |
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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: 29325.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Plasmid: pET26b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1C7D1G9*PLUS #2: RNA chain | | Mass: 24332.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | 142nd residue in the original sequence is PYL(PYRROLYSINE). This is (PYL)142W mutant. The residues ...142nd residue in the original sequence is PYL(PYRROLYSIN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, tri-potassium citrate / PH range: 7.5 - 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 22669 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rsym value: 0.103 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WBZ, 1EHZ Resolution: 2.703→42.762 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.703→42.762 Å
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Refine LS restraints |
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LS refinement shell |
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