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- PDB-8k7w: Crystal structure of Broccoli aptamer with DFHBI-1T -

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Basic information

Entry
Database: PDB / ID: 8k7w
TitleCrystal structure of Broccoli aptamer with DFHBI-1T
ComponentsRNA (49-MER)
KeywordsRNA / Fluorescent RNA Aptamer / Broccoli / DFHBI-1T
Function / homologyChem-2ZY / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsPeng, X. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: A general strategy for engineering GU base pairs to facilitate RNA crystallization.
Authors: Ren, Y. / Lin, X. / Liao, W. / Peng, X. / Deng, J. / Zhang, Z. / Zhan, J. / Zhou, Y. / Westhof, E. / Lilley, D.M.J. / Wang, J. / Huang, L.
History
DepositionJul 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (49-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3587
Polymers15,8741
Non-polymers4836
Water25214
1
A: RNA (49-MER)
hetero molecules

A: RNA (49-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,71614
Polymers31,7492
Non-polymers96712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1760 Å2
ΔGint-43 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.301, 35.006, 51.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: RNA chain RNA (49-MER)


Mass: 15874.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-2ZY / (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one


Mass: 320.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9F5N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.04 M Lithium chloride, 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0. ...Details: 0.04 M Lithium chloride, 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.24→32.78 Å / Num. obs: 8516 / % possible obs: 99 % / Redundancy: 5.73 % / Biso Wilson estimate: 25.166 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.037 / Net I/σ(I): 10.2
Reflection shellResolution: 2.24→2.32 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 785 / CC1/2: 0.583 / Rpim(I) all: 0.332 / % possible all: 93.23

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→32.78 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 410 4.82 %
Rwork0.2364 --
obs0.2381 8501 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→32.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1053 27 14 1094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061200
X-RAY DIFFRACTIONf_angle_d1.2081870
X-RAY DIFFRACTIONf_dihedral_angle_d16.252589
X-RAY DIFFRACTIONf_chiral_restr0.061245
X-RAY DIFFRACTIONf_plane_restr0.00751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.560.35071360.34012583X-RAY DIFFRACTION98
2.56-3.230.35111620.29662661X-RAY DIFFRACTION100
3.23-32.780.21931120.20052847X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.4896 Å / Origin y: 6.1287 Å / Origin z: 13.4987 Å
111213212223313233
T0.3629 Å2-0.0003 Å20.0643 Å2-0.3304 Å2-0.0048 Å2--0.3948 Å2
L2.3485 °2-0.2497 °21.4782 °2-0.8862 °2-0.7697 °2--2.9113 °2
S-0.288 Å °0.0201 Å °0.0429 Å °-0.0318 Å °0.0191 Å °-0.0983 Å °-0.0911 Å °0.0277 Å °0.2745 Å °
Refinement TLS groupSelection details: all

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