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- PDB-7els: Crystal structure of xanthine riboswitch with 8-azaxanthine -

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Basic information

Entry
Database: PDB / ID: 7els
TitleCrystal structure of xanthine riboswitch with 8-azaxanthine
ComponentsNMT1_8-azaxanthine (46-MER)
KeywordsRNA / riboswitch / 8-azaxanthine
Function / homology8-AZAXANTHINE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciesIdeonella sp. B508-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsXu, X.C. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionApr 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NMT1_8-azaxanthine (46-MER)
B: NMT1_8-azaxanthine (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,78619
Polymers29,1182
Non-polymers1,66917
Water82946
1
B: NMT1_8-azaxanthine (46-MER)
hetero molecules

A: NMT1_8-azaxanthine (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,78619
Polymers29,1182
Non-polymers1,66917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_457x-1,y,z+21
Buried area2920 Å2
ΔGint-97 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.721, 93.052, 40.052
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain NMT1_8-azaxanthine (46-MER)


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 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES, pH 6.0, 0.2 M calcium acetate, 10% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.102 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 7789 / % possible obs: 98.6 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.043 / Rrim(I) all: 0.143 / Χ2: 1.318 / Net I/σ(I): 4 / Num. measured all: 91238
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.81-2.9191.1126880.7860.3691.1770.56989
2.91-3.03100.7177430.920.2280.7540.68398.9
3.03-3.16110.4657840.9650.1420.4870.94499.5
3.16-3.3312.30.367750.9840.1070.3761.01999.2
3.33-3.5413.10.3247490.9660.0950.3381.08899.7
3.54-3.81130.247850.9870.0710.251.24899.9
3.81-4.2120.1877820.9690.0570.1961.429100
4.2-4.8130.167950.990.0470.1671.545100
4.8-6.0512.30.1248100.9950.0370.131.837100
6.05-5011.20.0968780.9970.0320.1012.29699.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ELP

7elp


Resolution: 3→40.05 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 36.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2741 341 5.41 %
Rwork0.2323 5966 -
obs0.2344 6307 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.9 Å2 / Biso mean: 84.6421 Å2 / Biso min: 54.4 Å2
Refinement stepCycle: final / Resolution: 3→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1998 35 46 2079
Biso mean--77.29 78.69 -
Num. residues----92
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.780.34981640.247729023066
3.78-40.050.25311770.227430643241

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