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- PDB-7elr: Crystal structure of xanthine riboswitch with xanthine -

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Basic information

Entry
Database: PDB / ID: 7elr
TitleCrystal structure of xanthine riboswitch with xanthine
ComponentsNMT1 (46-MER)
KeywordsRNA / riboswitch / xanthine
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / XANTHINE / RNA / RNA (> 10)
Function and homology information
Biological speciesIdeonella sp. B508-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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 (46-MER)
B: NMT1 (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,83321
Polymers29,1182
Non-polymers1,71519
Water97354
1
A: NMT1 (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,42811
Polymers14,5591
Non-polymers87010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-8 kcal/mol
Surface area8040 Å2
MethodPISA
2
B: NMT1 (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,40410
Polymers14,5591
Non-polymers8459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-7 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.439, 96.247, 41.475
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 (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-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
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: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.66-2.769.61.0478160.9120.32110.44984.9
2.76-2.8710.10.8298880.9220.2560.870.41695.4
2.87-311.40.479680.9840.1410.4920.46199.3
3-3.15120.2529360.9910.0750.2640.537100
3.15-3.3512.90.1679650.9960.0480.1740.653100
3.35-3.6113.30.1439630.9970.040.1490.69499.9
3.61-3.97130.1139650.9970.0320.1180.89100
3.97-4.5512.50.1029900.9960.0290.1060.995100
4.55-5.7312.80.0929930.9960.0270.0951.15699.9
5.73-5011.40.0810750.9940.0260.0841.46199.7

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Processing

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

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
RfactorNum. reflection% reflection
Rfree0.2648 476 5.05 %
Rwork0.2433 8951 -
obs0.2443 9427 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.25 Å2 / Biso mean: 100.0237 Å2 / Biso min: 61.76 Å2
Refinement stepCycle: final / Resolution: 2.66→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1998 37 54 2089
Biso mean--93.17 94.34 -
Num. residues----92
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.66-3.050.37351500.35842753290392
3.05-3.840.2871640.27143018318299
3.84-48.120.24321620.22163180334299

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