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Yorodumi- PDB-7lng: TNA modification at 3' end of RNA primer complex with guanosine d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lng | |||||||||||||||||||||||||||||||
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Title | TNA 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 | DIGUANOSINE-5'-TRIPHOSPHATE / Chem-LCC / Chem-LCG / Chem-LKC / Chem-TG / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 7lng.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lng.ent.gz | 21.6 KB | Display | PDB format |
PDBx/mmJSON format | 7lng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lng_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 7lng_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 7lng_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 7lng_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/7lng ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lng | HTTPS FTP |
-Related structure data
Related structure data | 7kukC 7kulC 7kumC 7kunC 7kuoC 7kupC 7lneC 7lnfC 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
-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 , 5 types, 12 molecules
#2: Chemical | ChemComp-LCC / [( #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | |
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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: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium pH 7.5, 1.5 M Lithium sulfate monohydrate |
-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 twin |
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Reflection | Resolution: 2.2→82.83 Å / Num. obs: 5325 / % possible obs: 99.68 % / Redundancy: 8.9 % / Biso Wilson estimate: 57.59 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.04 / Rrim(I) all: 0.111 / Net I/σ(I): 20 | ||||||||||||||||||
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 266 / CC1/2: 0.955 / Rpim(I) all: 0.101 / Rrim(I) all: 0.312 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UEE Resolution: 2.2→82.83 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.994 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.048 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: 55.478 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→82.83 Å
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Refine LS restraints |
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LS refinement shell |
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