+Open data
-Basic information
Entry | Database: PDB / ID: 5axm | ||||||
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Title | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) | ||||||
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: 2.21 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 | 5axm.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5axm.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 5axm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5axm_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 5axm_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | 5axm_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 5axm_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/5axm ftp://data.pdbj.org/pub/pdb/validation_reports/ax/5axm | HTTPS FTP |
-Related structure data
Related structure data | 5axkC 5axlC 5axnC 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: 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: 2.08 Å3/Da / Density % sol: 40.86 % |
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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-17A / Wavelength: 0.97319 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97319 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. obs: 35102 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rsym value: 0.09 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.21→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 3.2 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WBZ, 1EHZ Resolution: 2.21→48.144 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.57 / 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: 2.21→48.144 Å
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Refine LS restraints |
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LS refinement shell |
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