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Yorodumi- PDB-4pzk: Crystal strucrure of putative RNA methyltransferase from Bacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pzk | ||||||
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Title | Crystal strucrure of putative RNA methyltransferase from Bacillus anthracis. | ||||||
Components | tRNA (cytidine(34)-2'-O)-methyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-alpha sandwich / methyltransferase | ||||||
Function / homology | Function and homology information tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal strucrure of putative RNA methyltransferase from Bacillus anthracis. Authors: Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pzk.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pzk.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 4pzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pzk_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4pzk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4pzk_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 4pzk_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/4pzk ftp://data.pdbj.org/pub/pdb/validation_reports/pz/4pzk | HTTPS FTP |
-Related structure data
Related structure data | 3l8uS S: Starting model for refinement |
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Similar structure data | |
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: 19773.232 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS0516, BA_0547, cspR, GBAA_0547 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic References: UniProt: Q81YT5, UniProt: A0A6L7HQJ3*PLUS, tRNA (cytidine34-2'-O)-methyltransferase #2: Chemical | #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: 2.03 Å3/Da / Density % sol: 39.45 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M MgCl2; 0.1M Tris pH 8.5, 16% PEG 4000, 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-BM / Wavelength: 0.97916 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2014 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→31.6 Å / Num. all: 51748 / Num. obs: 51749 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.047 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2189 / Rsym value: 0.564 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L8U Resolution: 1.5→31.551 Å / SU ML: 0.13 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.89 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→31.551 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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