+Open data
-Basic information
Entry | Database: PDB / ID: 7elr | ||||||
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Title | Crystal structure of xanthine riboswitch with xanthine | ||||||
Components | NMT1 (46-MER) | ||||||
Keywords | RNA / riboswitch / xanthine | ||||||
Function / homology | GUANOSINE-5'-TRIPHOSPHATE / XANTHINE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Ideonella sp. B508-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | ||||||
Authors | Xu, X.C. / Ren, A.M. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition. Authors: Xu, X. / Egger, M. / Chen, H. / Bartosik, K. / Micura, R. / Ren, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7elr.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7elr.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 7elr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7elr_validation.pdf.gz | 5.4 MB | Display | wwPDB validaton report |
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Full document | 7elr_full_validation.pdf.gz | 5.4 MB | Display | |
Data in XML | 7elr_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 7elr_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/7elr ftp://data.pdbj.org/pub/pdb/validation_reports/el/7elr | HTTPS FTP |
-Related structure data
Related structure data | 7elpSC 7elqC 7elsC 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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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 14558.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sp. B508-1 (bacteria) Production host: in vitro transcription vector pT7-TP(deltai) (others) #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.39 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES, pH 6.0, 0.2 M calcium acetate, 10% (v/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.102 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.102 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.66→50 Å / Num. obs: 9559 / % possible obs: 98 % / Redundancy: 12 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.031 / Rrim(I) all: 0.105 / Χ2: 0.802 / Net I/σ(I): 4.2 / Num. measured all: 114293 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ELP Resolution: 2.66→48.12 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 41.99 / 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: 161.25 Å2 / Biso mean: 100.0237 Å2 / Biso min: 61.76 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.66→48.12 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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