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Yorodumi- PDB-6b3k: Crystal structure of mutant Spinach RNA aptamer in complex with F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b3k | |||||||||
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Title | Crystal structure of mutant Spinach RNA aptamer in complex with Fab BL3-6 | |||||||||
Components |
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Keywords | immune system/rna / RNA aptamer / Fragment of antibody / Chaperone-assisted RNA Crystallography / immune system-rna complex | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | |||||||||
Authors | DasGupta, S. / Koirala, D. / Shelke, S.A. / Piccirilli, J.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography. Authors: Koirala, D. / Shelke, S.A. / Dupont, M. / Ruiz, S. / DasGupta, S. / Bailey, L.J. / Benner, S.A. / Piccirilli, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b3k.cif.gz | 153.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b3k.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 6b3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b3k_validation.pdf.gz | 464.3 KB | Display | wwPDB validaton report |
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Full document | 6b3k_full_validation.pdf.gz | 469.2 KB | Display | |
Data in XML | 6b3k_validation.xml.gz | 22 KB | Display | |
Data in CIF | 6b3k_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/6b3k ftp://data.pdbj.org/pub/pdb/validation_reports/b3/6b3k | HTTPS FTP |
-Related structure data
Related structure data | 6b14C 4kzeS 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
#1: Antibody | Mass: 23852.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 23394.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: RNA chain | Mass: 26933.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.36 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 8% Tacsimate (pH 7.0), 20% Polyethylene glycol 3,350, 0.1 M HEPES (pH 7.2) |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→69.1 Å / Num. obs: 58291 / % possible obs: 97.6 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.09→2.165 Å / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.996 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KZE Resolution: 2.09→69.097 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→69.097 Å
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Refine LS restraints |
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LS refinement shell |
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