+Open data
-Basic information
Entry | Database: PDB / ID: 3a27 | ||||||
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Title | Crystal structure of M. jannaschii TYW2 in complex with AdoMet | ||||||
Components | Uncharacterized protein MJ1557 | ||||||
Keywords | TRANSFERASE / Wybutosine modification | ||||||
Function / homology | Function and homology information tRNAPhe (4-demethylwyosine37-C7) aminocarboxypropyltransferase / tRNA 4-demethylwyosine alpha-amino-alpha-carboxypropyltransferase activity / tRNA methyltransferase activity / transferase activity, transferring alkyl or aryl (other than methyl) groups / tRNA modification / tRNA methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å | ||||||
Authors | Umitsu, M. / Nishimasu, H. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2 Authors: Umitsu, M. / Nishimasu, H. / Noma, A. / Suzuki, T. / Ishitani, R. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a27.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a27.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 3a27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a27_validation.pdf.gz | 688.2 KB | Display | wwPDB validaton report |
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Full document | 3a27_full_validation.pdf.gz | 695.6 KB | Display | |
Data in XML | 3a27_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 3a27_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/3a27 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/3a27 | HTTPS FTP |
-Related structure data
Related structure data | 3a25C 3a26C 2frn 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: 31912.244 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ1557 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q58952 |
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#2: Chemical | ChemComp-SAM / |
#3: 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: 2.44 Å3/Da / Density % sol: 49.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 0.1M ammonium sulfate, 15% PEG5000, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 19841 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FRN 2frn Resolution: 2.005→43.446 Å / SU ML: 0.27 / σ(F): 1.52
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Solvent computation | Shrinkage radii: 0.9 Å / Bsol: 62.574 Å2 / ksol: 0.357 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.005→43.446 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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