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- PDB-9lmc: Crystal structure of Guanine-II riboswitch in complex with guanin... -

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Basic information

Entry
Database: PDB / ID: 9lmc
TitleCrystal structure of Guanine-II riboswitch in complex with guanine soaked with Mn2+
ComponentsPRTg (71-MER)
KeywordsRNA / guanine-II riboswitch / 2'-deoxyguanosine
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / GUANINE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesPaenibacillus sp. FSL E2-0178 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsLi, H.C. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Ligand specificity and adaptability revealed by the first Guanine-II riboswitch tertiary structure.
Authors: Li, H. / Shen, X. / Xu, X. / Tai, X. / He, M. / Zhang, J. / Ren, A.
History
DepositionJan 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRTg (71-MER)
B: PRTg (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,94915
Polymers45,6052
Non-polymers1,34413
Water55831
1
A: PRTg (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2838
Polymers22,8031
Non-polymers4817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PRTg (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6667
Polymers22,8031
Non-polymers8636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.425, 37.719, 94.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-104-

MN

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain PRTg (71-MER)


Mass: 22802.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. FSL E2-0178 (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)

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Non-polymers , 5 types, 44 molecules

#2: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Sodium chloride, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1.54975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54975 Å / Relative weight: 1
ReflectionResolution: 2.97→119.43 Å / Num. obs: 18498 / % possible obs: 99.4 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.056 / Rrim(I) all: 0.121 / Net I/σ(I): 10.5
Reflection shellResolution: 2.97→3.13 Å / Rmerge(I) obs: 0.424 / Num. unique obs: 1280 / CC1/2: 0.976 / Rpim(I) all: 0.255 / Rrim(I) all: 0.497

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
autoPROCdata reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→50.48 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2732 1685 10.12 %
Rwork0.2264 --
obs0.2313 16651 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.97→50.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3031 32 31 3094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063410
X-RAY DIFFRACTIONf_angle_d1.195305
X-RAY DIFFRACTIONf_dihedral_angle_d22.1231700
X-RAY DIFFRACTIONf_chiral_restr0.056709
X-RAY DIFFRACTIONf_plane_restr0.006144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.060.42021320.41191185X-RAY DIFFRACTION92
3.06-3.160.39721410.33171215X-RAY DIFFRACTION96
3.16-3.270.37421400.31671239X-RAY DIFFRACTION98
3.27-3.40.38071430.27831235X-RAY DIFFRACTION97
3.4-3.560.31451360.27341240X-RAY DIFFRACTION98
3.56-3.750.33271400.26881273X-RAY DIFFRACTION98
3.75-3.980.30071410.2431229X-RAY DIFFRACTION99
3.98-4.290.25661430.22041289X-RAY DIFFRACTION100
4.29-4.720.25781460.20181290X-RAY DIFFRACTION100
4.72-5.40.27131380.19451261X-RAY DIFFRACTION99
5.4-6.80.22121370.19251248X-RAY DIFFRACTION99
6.8-50.480.20491480.17461262X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -30.9806 Å / Origin y: 2.9136 Å / Origin z: -23.6254 Å
111213212223313233
T0.4271 Å20.0062 Å2-0.0571 Å2-0.5207 Å20.0087 Å2--0.5932 Å2
L-0.0557 °2-0.4833 °2-0.4678 °2-4.2457 °2-1.9006 °2--2.7467 °2
S0.0613 Å °-0.1463 Å °0.2892 Å °-0.341 Å °-0.4381 Å °-0.5527 Å °0.1466 Å °0.2436 Å °0.1764 Å °
Refinement TLS groupSelection details: all

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