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Yorodumi- PDB-7kuk: High resolution RNA primer complex with guanosine dinucleotide li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kuk | |||||||||||||||||||||||||||||||
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Title | High resolution RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | |||||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / nonenzymatic RNA extension | Function / homology | DIGUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | Authors | Fang, Z. / Giurgiu, C. / Szostak, J.W. | Funding support | United States, 2items |
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 | Title: Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis. Authors: Giurgiu, C. / Fang, Z. / Aitken, H.R.M. / Kim, S.C. / Pazienza, L. / Mittal, S. / Szostak, J.W. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kuk.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kuk.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 7kuk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kuk_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7kuk_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7kuk_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 7kuk_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/7kuk ftp://data.pdbj.org/pub/pdb/validation_reports/ku/7kuk | HTTPS FTP |
-Related structure data
Related structure data | 7kulC 7kumC 7kunC 7kuoC 7kupC 7lneC 7lnfC 7lngC 5ueeS 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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 4432.824 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate, 50 mM Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. obs: 13505 / % possible obs: 100 % / Redundancy: 18.5 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.009 / Rrim(I) all: 0.039 / Χ2: 1.006 / Net I/σ(I): 91.25 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 7 / Num. unique obs: 641 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.083 / Rrim(I) all: 0.339 / Χ2: 1.045 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UEE Resolution: 1.67→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.706 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.105 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.097 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→50 Å
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Refine LS restraints |
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LS refinement shell |
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