+Open data
-Basic information
Entry | Database: PDB / ID: 2dvi | ||||||
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Title | Complex structure of CCA-adding enzyme, mini-DCC and CTP | ||||||
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: 2.61 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 | 2dvi.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dvi.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/2dvi ftp://data.pdbj.org/pub/pdb/validation_reports/dv/2dvi | HTTPS FTP |
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-Related structure data
Related structure data | 2dr5C 2dr7C 2dr8C 2dr9SC 2draC 2drbC 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
-RNA chain / Protein , 2 types, 2 molecules BA
#1: RNA chain | Mass: 10904.503 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) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28126, EC: 2.7.7.25, EC: 2.7.7.21 |
-Non-polymers , 4 types, 177 molecules
#3: Chemical | ChemComp-SO4 / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-CTP / |
#6: 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: 2.91 Å3/Da / Density % sol: 57.71 % | ||||||||||||||||||||||||||||||||||||||||||||
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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 (NH4)2SO4, 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: 2.6→50 Å / Num. all: 23070 / Num. obs: 23070 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.7 Å2 |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DR9 Resolution: 2.61→9.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1934818.03 / 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: 41.8752 Å2 / ksol: 0.406663 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.61→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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