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Open data
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Basic information
Entry | Database: PDB / ID: 4kze | ||||||
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Title | Crystal structure of an RNA aptamer in complex with Fab | ||||||
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![]() | immune system/rna / G-quadruplex / Fluorescence / Fluorophore binding / immune system-rna complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, H. / Suslov, N.B. / Li, N. / Koldobskaya, Y. / Rice, P.A. / Piccirilli, J.A. | ||||||
![]() | ![]() Title: A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Authors: Huang, H. / Suslov, N.B. / Li, N.S. / Shelke, S.A. / Evans, M.E. / Koldobskaya, Y. / Rice, P.A. / Piccirilli, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.4 KB | Display | ![]() |
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PDB format | ![]() | 115.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 462.9 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-RNA chain , 1 types, 1 molecules R
#3: RNA chain | Mass: 27446.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Spinach RNA aptamer |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24665.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
-Non-polymers , 3 types, 277 molecules ![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-K / |
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#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 8% Tacsimate, 20% PEG 3,350, 0.1 M HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.2 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2013 |
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: 2.4→45.37 Å / Num. all: 38347 / Num. obs: 38273 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.066 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.9 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 2.404→45.366 Å
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Refine LS restraints |
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LS refinement shell |
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