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Yorodumi- PDB-1yzh: Crystal Structure of the Conserved Hypothetical Protein, Methyltr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yzh | ||||||
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Title | Crystal Structure of the Conserved Hypothetical Protein, Methyltransferase from Streptococcus pneumoniae TIGR4 | ||||||
Components | tRNA (guanine-N(7)-)-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / alpha-beta-alpha sandwich / S-adenosylmethionine-dependent / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å | ||||||
Authors | Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Conserved Methyltransferase from Streptococcus pneumoniae TIGR4 Authors: Kim, Y. / Li, H. / Collart, F. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHORS STATE THE BIOLOGICAL ASSEMBLY IS NOT CONFIRMED BY EXPERIMENT BUT IS MOST LIKELY A MONOMER AS SEEN IN OTHER SIMILAR METHYLTRANSFERASES (BY SEQUENCE AND STRUCTURES). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yzh.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yzh.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yzh ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yzh | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-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: 24870.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: trmB, SP0550 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: P67506, tRNA (guanine46-N7)-methyltransferase #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Citrate, PEG3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2005 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→36.5 Å / Num. all: 32537 / Num. obs: 31802 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3 / Num. unique all: 2390 / % possible all: 74.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.02→36.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.151 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CNS 1.1 was also used in refinement. Hydrogens have been added in the riding positions.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.733 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→36.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.022→2.075 Å / Total num. of bins used: 20
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