+Open data
-Basic information
Entry | Database: PDB / ID: 2zw9 | ||||||
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Title | Crystal structure of tRNA wybutosine synthesizing enzyme TYW4 | ||||||
Components | Leucine carboxyl methyltransferase 2 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase / tRNAPhe {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methoxycarbonyltransferase / wybutosine biosynthetic process / tRNA methyltransferase activity / tRNA modification / tRNA methylation / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Suzuki, Y. / Noma, A. / Suzuki, T. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2009 Title: Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Authors: Suzuki, Y. / 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 | 2zw9.cif.gz | 275.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zw9.ent.gz | 222 KB | Display | PDB format |
PDBx/mmJSON format | 2zw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zw9_validation.pdf.gz | 938.8 KB | Display | wwPDB validaton report |
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Full document | 2zw9_full_validation.pdf.gz | 967.1 KB | Display | |
Data in XML | 2zw9_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 2zw9_validation.cif.gz | 67.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/2zw9 ftp://data.pdbj.org/pub/pdb/validation_reports/zw/2zw9 | HTTPS FTP |
-Related structure data
Related structure data | 2zwaC 2zzkC 2zw8 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 79050.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PPM2, TYW4, YOL141W / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus References: UniProt: Q08282, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | AUTHORS CONSIDER THAT THIS DIFFERENCE MAY STEM FROM A POLYMORPHISM OF THE YEAST STRAIN OR SOME ...AUTHORS CONSIDER THAT THIS DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 200mM ammonium citrate (pH 7), 20% (w/v) PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-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: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 52008 / Num. obs: 52008 / % possible obs: 90.6 % / Redundancy: 4.1 % / Rsym value: 0.07 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.12 / Num. unique all: 2218 / Rsym value: 0.305 / % possible all: 76.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→46.322 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 26.36 / 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 / Bsol: 33.725 Å2 / ksol: 0.317 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.96 Å2 / Biso mean: 64.2 Å2 / Biso min: 25.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→46.322 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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