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Yorodumi- PDB-4yvi: Crystal Structure of H. influenzae TrmD in complex with sinefungi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yvi | ||||||
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Title | Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA | ||||||
Components |
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Keywords | TRANSFERASE/RNA / MTase / SPOUT / tRNA / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Yoshida, K. / Ito, T. / Yokoyama, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. Authors: Ito, T. / Masuda, I. / Yoshida, K. / Goto-Ito, S. / Sekine, S. / Suh, S.W. / Hou, Y.M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yvi.cif.gz | 153 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yvi.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yvi_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4yvi_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4yvi_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 4yvi_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/4yvi ftp://data.pdbj.org/pub/pdb/validation_reports/yv/4yvi | HTTPS FTP |
-Related structure data
Related structure data | 4yvgC 4yvhSC 4yvjC 4yvkC 3akzS 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: 29750.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria) Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: trmD, HI_0202 / Production host: Escherichia coli (E. coli) References: UniProt: P43912, tRNA (guanine37-N1)-methyltransferase #2: RNA chain | | Mass: 23858.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 12057205 #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: sodium acetate trihydrate, ammonium phosphate monobasic, PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 17898 / % possible obs: 99.6 % / Redundancy: 10.3 % / Net I/σ(I): 20.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YVH, 3AKZ Resolution: 3.01→34.529 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.489 Å2 / ksol: 0.307 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.01→34.529 Å
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Refine LS restraints |
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LS refinement shell |
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