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Yorodumi- PDB-4x4n: Crystal structure of the A.fulgidus CCA-adding enzyme in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x4n | ||||||
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Title | Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix | ||||||
Components |
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Keywords | transferase/RNA / protein-RNA complex / tRNA / non-coding RNA / CCA-adding enzyme / nucleotidyltransferase / ncRNA / 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) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.953 Å | ||||||
Authors | Kuhn, C.-D. / Joshua-Tor, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2015 Title: On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme. Authors: Kuhn, C.D. / Wilusz, J.E. / Zheng, Y. / Beal, P.A. / Joshua-Tor, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x4n.cif.gz | 751.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x4n.ent.gz | 626.9 KB | Display | PDB format |
PDBx/mmJSON format | 4x4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x4n_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4x4n_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4x4n_validation.xml.gz | 58.6 KB | Display | |
Data in CIF | 4x4n_validation.cif.gz | 80.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/4x4n ftp://data.pdbj.org/pub/pdb/validation_reports/x4/4x4n | HTTPS FTP |
-Related structure data
Related structure data | 4x4oC 4x4pC 4x4qC 4x4rC 4x4sC 4x4tC 4x4uC 4x4vC 4x4wC 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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Details | biological units are chains A+B and C+D |
-Components
-Protein , 1 types, 4 molecules ACEF
#1: Protein | Mass: 53672.484 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: cca, AF_2156 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL References: UniProt: O28126, CCA tRNA nucleotidyltransferase |
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-RNA chain , 2 types, 4 molecules GBDI
#2: RNA chain | Mass: 10302.164 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: RNA chain | | Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 4 types, 7 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GMP / | #6: Chemical | ChemComp-5GP / | #7: Chemical | ChemComp-GOL / | |
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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: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: 18.6% PEG4000, 0.2M tri-Lithium Citrate, 0.05M Hepes pH 7.75, 0.08M Ammonium Sulfate PH range: 7.75 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→30 Å / Num. obs: 53329 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 67.8 Å2 / Rmerge(I) obs: 0.056 / Χ2: 0.771 / Net I/av σ(I): 18.586 / Net I/σ(I): 8.1 / Num. measured all: 173434 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.953→29.885 Å / FOM work R set: 0.8076 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.31 / 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: 231.54 Å2 / Biso mean: 46.99 Å2 / Biso min: 2.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.953→29.885 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: 19
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