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Yorodumi- PDB-6b14: Crystal structure of Spinach RNA aptamer in complex with Fab BL3-6S97N -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b14 | |||||||||
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Title | Crystal structure of Spinach RNA aptamer in complex with Fab BL3-6S97N | |||||||||
Components |
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Keywords | immune system/rna / Spinach RNA aptamer / Antibody engineering / 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: 1.64 Å | |||||||||
Authors | DasGupta, S. / 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 | 6b14.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b14.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 6b14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b14_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 6b14_full_validation.pdf.gz | 469.2 KB | Display | |
Data in XML | 6b14_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 6b14_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/6b14 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/6b14 | HTTPS FTP |
-Related structure data
Related structure data | 6b3kC 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 |
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#2: Antibody | Mass: 23421.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli |
#3: RNA chain | Mass: 26941.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.57 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.1 M Succinic acid (pH 7.0), 12% Polyethylene glycol 3,350, room temperature. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97921 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→49.54 Å / Num. obs: 119527 / % possible obs: 97.89 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.64→1.7 Å / Mean I/σ(I) obs: 0.7 / Num. unique all: 11795 / CC1/2: 0.996 / % possible all: 97.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KZE Resolution: 1.64→49.54 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→49.54 Å
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Refine LS restraints |
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LS refinement shell |
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