+Open data
-Basic information
Entry | Database: PDB / ID: 3amu | ||||||
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Title | Crystal structure of the TiaS-tRNA(Ile2)-AMPCPP-agmatine complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / TiaS / tRNA(Ile2) / modification / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information tRNAIle2-agmatinylcytidine synthase / ligase activity, forming carbon-nitrogen bonds / tRNA wobble cytosine modification / nucleic acid binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Numata, T. / Osawa, T. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: Structural basis of tRNA agmatinylation essential for AUA codon decoding Authors: Osawa, T. / Kimura, S. / Terasaka, N. / Inanaga, H. / Suzuki, T. / Numata, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3amu.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3amu.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 3amu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3amu_validation.pdf.gz | 759.1 KB | Display | wwPDB validaton report |
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Full document | 3amu_full_validation.pdf.gz | 798.3 KB | Display | |
Data in XML | 3amu_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 3amu_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/3amu ftp://data.pdbj.org/pub/pdb/validation_reports/am/3amu | HTTPS FTP |
-Related structure data
Related structure data | 3amtSC 3au7C 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: 50543.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_2259 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O28025 |
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#2: RNA chain | Mass: 25122.984 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: in vitro transcription using T7 RNA polymerase, sequence naturally exist in Archaeoglobus fulgidus Source: (synth.) Archaeoglobus fulgidus (archaea) |
#3: Chemical | ChemComp-APC / |
#4: Chemical | ChemComp-AG2 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.085M Tris-HCl pH8.5, 0.17M sodium acetate, 28% PEG 4000, 15% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 26, 2009 / Details: mirrors |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 15880 / % possible obs: 99.7 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3AMT Resolution: 3.1→47.48 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 22650.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 16.3058 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→47.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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