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Yorodumi- PDB-3w1k: Crystal structure of the selenocysteine synthase SelA and tRNASec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w1k | ||||||
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Title | Crystal structure of the selenocysteine synthase SelA and tRNASec complex | ||||||
Components |
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Keywords | TRANSFERASE/RNA / protein-RNA complex / homodecamer / pentamer of dimers / fold-type I pyridoxal 5'-phosphate (PLP) dependent enzyme / non-canonical tRNA / L-seryl-tRNA(Sec) selenium transferase / selenocysteine synthesis / selenium metabolism / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information L-seryl-tRNASec selenium transferase / L-seryl-tRNA(Sec) selenium transferase activity / selenocysteine incorporation / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) Thermoanaerobacter tengcongensis MB4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.5 Å | ||||||
Authors | Itoh, Y. / Sekine, S. / Yokoyama, S. | ||||||
Citation | Journal: Science / Year: 2013 Title: Decameric SelA-tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation Authors: Itoh, Y. / Brocker, M.J. / Sekine, S. / Hammond, G. / Suetsugu, S. / Soll, D. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w1k.cif.gz | 694.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w1k.ent.gz | 561.2 KB | Display | PDB format |
PDBx/mmJSON format | 3w1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w1k_validation.pdf.gz | 500.6 KB | Display | wwPDB validaton report |
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Full document | 3w1k_full_validation.pdf.gz | 651.8 KB | Display | |
Data in XML | 3w1k_validation.xml.gz | 71 KB | Display | |
Data in CIF | 3w1k_validation.cif.gz | 107.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/3w1k ftp://data.pdbj.org/pub/pdb/validation_reports/w1/3w1k | HTTPS FTP |
-Related structure data
Related structure data | 3w1hSC 3w1iC 3w1jC 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: 50925.160 Da / Num. of mol.: 5 / Mutation: K19A, K21A, K46A, K48A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: selA / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) References: UniProt: O67140, L-seryl-tRNASec selenium transferase #2: RNA chain | Mass: 30492.035 Da / Num. of mol.: 5 / Source method: obtained synthetically Details: The tRNASec from Thermoanaerobacter tengcongensis MB4 was prepared by in vitro transcription with T7 RNA polymerase. Source: (synth.) Thermoanaerobacter tengcongensis MB4 (bacteria) References: GenBank: 20671658 |
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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: 4.85 Å3/Da / Density % sol: 74.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 35% ethylene glycol, 95mM NaNO3, 20mM Tris-HCl, 0.2M NaCl, 10mM MgCl2, 3mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 16, 2009 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 7.5→50 Å / Num. all: 9956 / Num. obs: 9777 / % possible obs: 98.2 % / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Biso Wilson estimate: 250 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 7.5→7.77 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 2.04 / Num. unique all: 990 / Rsym value: 0.712 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W1H Resolution: 7.5→49.94 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 7615012.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 314.482 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 525.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 7.5→49.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 7.5→7.97 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file |
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