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Open data
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Basic information
Entry | Database: PDB / ID: 7kd1 | ||||||
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Title | Apo structure of the THF riboswitch aptamer domain | ||||||
![]() | tetrahydrofolate riboswitch aptamer domain | ||||||
![]() | RNA / riboswitch / apo / gene regulation | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilt, H.M. / Stagno, J.R. / Wang, Y.-X. | ||||||
![]() | ![]() Title: Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation. Authors: Wilt, H.M. / Yu, P. / Tan, K. / Wang, Y.X. / Stagno, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.8 KB | Display | ![]() |
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PDB format | ![]() | 87.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414 KB | Display | ![]() |
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Full document | ![]() | 420.7 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lvvS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: RNA chain | Mass: 28849.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 100 mM MES, pH 5.6, 200 mM NaCl, 2.5 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.75 Å / Num. obs: 30818 / % possible obs: 98.73 % / Redundancy: 7.34 % / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.01 / Rrim(I) all: 0.028 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.07 % / Rmerge(I) obs: 3.639 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2962 / CC1/2: 0.488 / Rpim(I) all: 1.6 / Rrim(I) all: 3.985 / % possible all: 97.21 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LVV Resolution: 1.9→40.75 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.48 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 216.86 Å2 / Biso mean: 87.75 Å2 / Biso min: 43.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→40.75 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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