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Yorodumi- PDB-2hma: The Crystal Structure of tRNA (5-Methylaminomethyl-2-Thiouridylat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hma | ||||||
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Title | The Crystal Structure of tRNA (5-Methylaminomethyl-2-Thiouridylate)-Methyltransferase TrmU from Streptococcus pneumoniae | ||||||
Components | Probable tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase | ||||||
Keywords | TRANSFERASE / alpha-beta / beta barrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information tRNA-uridine 2-sulfurtransferase / sulfurtransferase activity / tRNA modification / tRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å | ||||||
Authors | Kim, Y. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of tRNA (5-Methylaminomethyl-2-Thiouridylate)-Methyltransferase TrmU from Streptococcus pneumoniae Authors: Kim, Y. / Zhou, M. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hma.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hma.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hma_validation.pdf.gz | 729.4 KB | Display | wwPDB validaton report |
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Full document | 2hma_full_validation.pdf.gz | 737.7 KB | Display | |
Data in XML | 2hma_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2hma_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/2hma ftp://data.pdbj.org/pub/pdb/validation_reports/hm/2hma | HTTPS FTP |
-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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Unit cell |
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-Components
#1: Protein | Mass: 42563.797 Da / Num. of mol.: 1 Fragment: tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: trmU / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: Q97T38, tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-SAM / |
#4: 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: 4.64 Å3/Da / Density % sol: 73.47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM Tris pH=8.5, and 3.5M NaFormate, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2006 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→44.73 Å / Num. all: 32091 / Num. obs: 31670 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.41→2.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.78 / Num. unique all: 2791 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.41→44.73 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.624 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.187 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.346 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→44.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.472 Å / Total num. of bins used: 20 /
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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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