+Open data
-Basic information
Entry | Database: PDB / ID: 4x0b | ||||||
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Title | Structure of tRNA-processing enzyme complex 7 | ||||||
Components |
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Keywords | TRANSFERASE/RNA / RNA Nucleotidyltransferase / CCA-adding enzyme / A-adding enzyme / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity / RNA 3'-end processing / tRNA processing / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Yamashita, S. / Tomita, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Structure / Year: 2015 Title: Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme. Authors: Yamashita, S. / Martinez, A. / Tomita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x0b.cif.gz | 258.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x0b.ent.gz | 208 KB | Display | PDB format |
PDBx/mmJSON format | 4x0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x0b_validation.pdf.gz | 463.5 KB | Display | wwPDB validaton report |
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Full document | 4x0b_full_validation.pdf.gz | 473.5 KB | Display | |
Data in XML | 4x0b_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 4x0b_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/4x0b ftp://data.pdbj.org/pub/pdb/validation_reports/x0/4x0b | HTTPS FTP |
-Related structure data
Related structure data | 4wbyC 4wbzC 4wc0C 4wc1C 4wc2C 4wc3SC 4wc4C 4wc5C 4wc6C 4wc7C 4x0aC 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: Protein | Mass: 46550.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: pcnB1, aq_411 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66728 |
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#2: RNA chain | Mass: 24805.738 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: isopropanol, potassium chloride, magnesium chloride, sodium cacodylate |
-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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. obs: 14222 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.163 / Rsym value: 0.151 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.4 / Rsym value: 1.752 / Rejects: 0 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WC3 Resolution: 3.2→19.859 Å / FOM work R set: 0.6255 / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 577.92 Å2 / Biso mean: 230.77 Å2 / Biso min: 77.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→19.859 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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