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Yorodumi- PDB-2dr5: Complex structure of CCA adding enzyme with mini-helix lacking CCA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dr5 | ||||||
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Title | Complex structure of CCA adding enzyme with mini-helix lacking CCA | ||||||
Components |
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Keywords | TRANSFERASE/RNA / protein-rna complex / TRANSFERASE-RNA COMPLEX | ||||||
Function / homology | Function and homology information tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Tomita, K. / Ishitani, R. / Fukai, S. / Nureki, O. | ||||||
Citation | Journal: Nature / Year: 2006 Title: Complete crystallographic analysis of the dynamics of CCA sequence addition Authors: Tomita, K. / Ishitani, R. / Fukai, S. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dr5.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dr5.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dr5_validation.pdf.gz | 470 KB | Display | wwPDB validaton report |
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Full document | 2dr5_full_validation.pdf.gz | 487.9 KB | Display | |
Data in XML | 2dr5_validation.xml.gz | 22 KB | Display | |
Data in CIF | 2dr5_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/2dr5 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/2dr5 | HTTPS FTP |
-Related structure data
Related structure data | 2dr7C 2dr8C 2dr9C 2draC 2drbC 2dviC 1uetS C: citing same article (ref.) S: Starting model for refinement |
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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: RNA chain | Mass: 10294.140 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Protein | Mass: 51469.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O28126, EC: 2.7.7.25, EC: 2.7.7.21 | ||
#3: Chemical | #4: 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: 3.02 Å3/Da / Density % sol: 59.26 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 50mM HEPES, 20% PEG 3550, 0.2M Tri-lithium citrate, 80mM NH4SO4, pH 7.5, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2005 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 19376 / Num. obs: 19376 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 80 Å2 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UET Resolution: 2.8→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2888737.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.280021 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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