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Yorodumi- PDB-5a7z: Crystal structure of Sulfolobus acidocaldarius Trm10 at 2.1 angst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a7z | ||||||
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Title | Crystal structure of Sulfolobus acidocaldarius Trm10 at 2.1 angstrom resolution. | ||||||
Components | TRNA (ADENINE(9)-N1)-METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / SPOUT / TRM10 / TRNA METHYLTRANSFERASE | ||||||
Function / homology | Function and homology information tRNA (adenine9-N1)-methyltransferase / tRNA (adenine(9)-N1)-methyltransferase activity / tRNA methylation / tRNA processing / cytoplasm Similarity search - Function | ||||||
Biological species | SULFOLOBUS ACIDOCALDARIUS (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Van Laer, B. / Roovers, M. / Wauters, L. / Kasprzak, J. / Dyzma, M. / Deyaert, E. / Feller, A. / Bujnicki, J. / Droogmans, L. / Versees, W. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Structural and Functional Insights Into tRNA Binding and Adenosine N1-Methylation by an Archaeal Trm10 Homologue. Authors: Van Laer, B. / Roovers, M. / Wauters, L. / Kasprzak, J.M. / Dyzma, M. / Deyaert, E. / Kumar Singh, R. / Feller, A. / Bujnicki, J.M. / Droogmans, L. / Versees, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a7z.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a7z.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 5a7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a7z_validation.pdf.gz | 426.3 KB | Display | wwPDB validaton report |
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Full document | 5a7z_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 5a7z_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 5a7z_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/5a7z ftp://data.pdbj.org/pub/pdb/validation_reports/a7/5a7z | HTTPS FTP |
-Related structure data
Related structure data | 5a7tSC 5a7yC S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 30534.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic) Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: Q4J894, tRNA (adenine9-N1)-methyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 2 % DIOXANE, 0.05 M BICINE PH 9, 15 % PEG20K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97926 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.9 Å / Num. obs: 16213 / % possible obs: 99.4 % / Observed criterion σ(I): 1.5 / Redundancy: 8.6 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 9.23 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.68 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 1.74 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A7T Resolution: 2.1→69.11 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 43.559 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→69.11 Å
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Refine LS restraints |
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