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- PDB-7elq: Crystal structure of xanthine riboswitch with xanthine, manganese saok -

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Basic information

Entry
Database: PDB / ID: 7elq
TitleCrystal structure of xanthine riboswitch with xanthine, manganese saok
ComponentsNMT1_Mn (46-MER)
KeywordsRNA / riboswitch / xanthine / manganese saok
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: 2.6 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

Downloads & links

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Assembly

Deposited unit
A: NMT1_Mn (46-MER)
B: NMT1_Mn (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,12623
Polymers29,1182
Non-polymers2,00921
Water1,44180
1
A: NMT1_Mn (46-MER)
hetero molecules

B: NMT1_Mn (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,12623
Polymers29,1182
Non-polymers2,00921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_657x+1,y,z+21
Buried area3630 Å2
ΔGint-108 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.472, 92.944, 40.298
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 46
211chain BB1 - 46

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain NMT1_Mn (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)

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Non-polymers , 5 types, 101 molecules

#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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 51.87 %
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: 1.2398 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: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13965 / % possible obs: 80.3 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.044 / Rrim(I) all: 0.148 / Χ2: 1.142 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6950.6243300.5120.2710.6860.45134.6
2.69-2.87.10.6344200.650.2350.680.51345.4
2.8-2.938.10.565470.7510.190.5940.58457.5
2.93-3.088.40.4387460.9130.1430.4630.87678.4
3.08-3.289.50.3479120.9580.1110.3661.07496.1
3.28-3.5310.90.3119270.9720.0970.3261.09797.4
3.53-3.8812.10.2469330.9770.0740.2581.23396.2
3.88-4.4512.10.2019640.9830.060.211.3598.3
4.45-5.6120.1499700.990.0440.1561.36698.2
5.6-5011.50.074103110.0230.0781.28497

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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: 2.6→46.47 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 734 5.26 %
Rwork0.2106 13231 -
obs0.2133 13965 78.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.55 Å2 / Biso mean: 55.6593 Å2 / Biso min: 36.69 Å2
Refinement stepCycle: final / Resolution: 2.6→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1998 39 80 2117
Biso mean--53.64 53.29 -
Num. residues----92
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1102X-RAY DIFFRACTION9.534TORSIONAL
12B1102X-RAY DIFFRACTION9.534TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.80.4129610.35341249131037
2.8-3.090.35311210.28552199232065
3.09-3.530.22921770.24733211338897
3.53-4.450.27021780.20053307348598
4.45-46.470.24481970.18083265346298

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