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- PDB-7elp: Crystal structure of xanthine riboswitch with xanthine, iridium h... -

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Basic information

Entry
Database: PDB / ID: 7elp
TitleCrystal structure of xanthine riboswitch with xanthine, iridium hexammine soak
ComponentsNMT1_Ir(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 / SAD / Resolution: 2.79 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 1.2May 29, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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_Ir(46-MER)
B: NMT1_Ir(46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,43425
Polymers29,1182
Non-polymers2,31623
Water1,53185
1
A: NMT1_Ir(46-MER)
hetero molecules

B: NMT1_Ir(46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,43425
Polymers29,1182
Non-polymers2,31623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_657x+1,y,z+21
Buried area3330 Å2
ΔGint-129 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.465, 100.192, 40.267
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain NMT1_Ir(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, 108 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-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ir / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-XAN / XANTHINE


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


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.75 Å3/Da / Density % sol: 55.32 %
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: Jul 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 15338 / % possible obs: 99.8 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.042 / Rrim(I) all: 0.141 / Χ2: 2.428 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.911.61.2278220.7090.3691.2830.40799.2
2.9-3.0213.10.6568200.9610.1850.6820.438100
3.02-3.1513.10.3248400.9870.0920.3370.519100
3.15-3.32130.2048280.9920.0580.2130.563100
3.32-3.5312.80.1588210.9940.0450.1650.77100
3.53-3.811.90.1098450.9920.0320.1141.214100
3.8-4.1813.40.0968500.9910.0270.0991.605100
4.18-4.79130.088450.9970.0230.0831.937100
4.79-6.0311.80.0798710.9920.0230.0823.46499.8
6.03-5011.80.1519350.9810.0490.15912.92299.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.79→39.73 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 808 5.27 %
Rwork0.215 14530 -
obs0.2181 15338 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.16 Å2 / Biso mean: 84.6506 Å2 / Biso min: 54.91 Å2
Refinement stepCycle: final / Resolution: 2.79→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1998 41 85 2124
Biso mean--79.62 82.62 -
Num. residues----92
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.79-2.960.48211300.378235096
2.96-3.190.31851430.23222448100
3.19-3.510.31441480.25752401100
3.51-4.020.31151260.21012492100
4.02-5.060.28821260.21132439100
5.06-39.730.22021350.1904240098

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