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Yorodumi- PDB-7lne: ANA modification at 3' end of RNA primer complex with guanosine d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lne | |||||||||||||||||||||||||||||||
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Title | ANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | |||||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / nonenzymatic RNA extension | Function / homology | GUANINE ARABINOSE-5'-PHOSPHATE / DIGUANOSINE-5'-TRIPHOSPHATE / Chem-LCC / Chem-LCG / Chem-LKC / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 | 7lne.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lne.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lne_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 7lne_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 7lne_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 7lne_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/7lne ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lne | HTTPS FTP |
-Related structure data
Related structure data | 7kukC 7kulC 7kumC 7kunC 7kuoC 7kupC 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
-RNA chain , 1 types, 2 molecules AB
#1: RNA chain | Mass: 4422.683 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 7 types, 115 molecules
#2: Chemical | ChemComp-LCC / [( #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
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: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.7 M Lithium sulfate, 10 % w/v Glycerol |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033175 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033175 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 14626 / % possible obs: 98.7 % / Redundancy: 5.8 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Χ2: 0.923 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 691 / CC1/2: 0.973 / CC star: 0.993 / Rpim(I) all: 0.106 / Rrim(I) all: 0.226 / Χ2: 0.8 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UEE Resolution: 1.53→37.621 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.279 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.086 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: 16.202 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→37.621 Å
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Refine LS restraints |
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LS refinement shell |
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