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Yorodumi- PDB-3au7: Crystal structure of the ZRD-deleted mutant of TiaS in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3au7 | ||||||
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Title | Crystal structure of the ZRD-deleted mutant of TiaS in complex with agmatine | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | RNA BINDING PROTEIN / ATP hydrolysis | ||||||
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: 2.6 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 | 3au7.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3au7.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 3au7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/3au7 ftp://data.pdbj.org/pub/pdb/validation_reports/au/3au7 | HTTPS FTP |
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-Related structure data
Related structure data | 3amtSC 3amuC 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: 45905.328 Da / Num. of mol.: 1 / Mutation: Deletion of UNP residues 344-385 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: Chemical | ChemComp-AG2 / |
#3: 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: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 17.1% PEG 4000, 18% 2-propanol, 0.09M sodium citrate pH5.6, 0.5M sodium chloride, 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: Feb 8, 2010 / Details: mirrors |
Radiation | Monochromator: Numeric 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: 2.6→50 Å / Num. obs: 15338 / % possible obs: 99.8 % / Redundancy: 14.8 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.3 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3AMT Resolution: 2.6→48.73 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 77944.13 / 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: 39.9907 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→48.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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