+Open data
-Basic information
Entry | Database: PDB / ID: 7mkt | ||||||||||||||||||||||||||||
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Title | Crystal structure of r(GU)11G-NMM complex | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / RNA-porpyrin complex | Function / homology | : / N-METHYLMESOPORPHYRIN / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å | Authors | Bingman, C.A. / Roschdi, S. / Nomura, Y. / Butcher, S.E. | Funding support | United States, 1items |
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2022 | Title: An atypical RNA quadruplex marks RNAs as vectors for gene silencing. Authors: Roschdi, S. / Yan, J. / Nomura, Y. / Escobar, C.A. / Petersen, R.J. / Bingman, C.A. / Tonelli, M. / Vivek, R. / Montemayor, E.J. / Wickens, M. / Kennedy, S.G. / Butcher, S.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mkt.cif.gz | 33 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mkt.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 7mkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mkt_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7mkt_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7mkt_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 7mkt_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/7mkt ftp://data.pdbj.org/pub/pdb/validation_reports/mk/7mkt | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 7465.337 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) | ||
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#2: Chemical | ChemComp-MMP / | ||
#3: Chemical | ChemComp-K / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: The RNA smaple was prepared by mixing 1.44mM (GU)11G RNA and 1.44 mM NMM in 10 mM Tris, pH 7.03, and 100 mM KCl. An equal volume of RNA sample solution and reservoir solution were mixed and ...Details: The RNA smaple was prepared by mixing 1.44mM (GU)11G RNA and 1.44 mM NMM in 10 mM Tris, pH 7.03, and 100 mM KCl. An equal volume of RNA sample solution and reservoir solution were mixed and suspended over the reservoir solution consisting of 0.5 M Na/K tartarate, 0.1 M TrisHCl, pH 8.5, 5 mM NaOH. Cryoprotection: reservoir solution supplemented with 30% ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å | |||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 27, 2020 | |||||||||||||||||||||||||
Radiation | Monochromator: Si <111> / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.97→21.61 Å / Num. obs: 5407 / % possible obs: 99.02 % / Redundancy: 6.7 % / Biso Wilson estimate: 63.54 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.05163 / Rpim(I) all: 0.0231 / Rrim(I) all: 0.05684 / Net I/σ(I): 16.09 | |||||||||||||||||||||||||
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.7553 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 529 / CC1/2: 0.966 / CC star: 0.991 / Rpim(I) all: 0.3083 / Rrim(I) all: 0.8172 / % possible all: 99.25 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.97→21.61 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.968 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Authors state that 4-way twin law was applied during refinement, while the validation program recalculated with different twin law. This causes the discrepancies between calculated and ...Details: Authors state that 4-way twin law was applied during refinement, while the validation program recalculated with different twin law. This causes the discrepancies between calculated and reported Rwork/Rfree values.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.361 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→21.61 Å
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Refine LS restraints |
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