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- PDB-8hzd: A new fluorescent RNA aptamer bound with N618 -

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Basic information

Entry
Database: PDB / ID: 8hzd
TitleA new fluorescent RNA aptamer bound with N618
Components(RNA (36-MER)) x 2
KeywordsRNA / fluorescent RNA aptamer
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSong, Q.Q. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift.
Authors: Huang, K. / Song, Q. / Fang, M. / Yao, D. / Shen, X. / Xu, X. / Chen, X. / Zhu, L. / Yang, Y. / Ren, A.
History
DepositionJan 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (36-MER)
B: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,22111
Polymers23,3202
Non-polymers9019
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-61 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.494, 46.461, 56.251
Angle α, β, γ (deg.)90.00, 113.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (36-MER)


Mass: 11620.019 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: RNA chain RNA (36-MER)


Mass: 11699.999 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-O2I / 4-[(~{E})-2-[(4~{Z})-4-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]methylidene]-1-methyl-5-oxidanylidene-imidazol-2-yl]ethenyl]benzenecarbonitrile


Mass: 365.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H13F2N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.89 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Magnesium Chloride, 0.1 M HEPES pH7.5, 30%(w/v) PEGmm550, 0.001 M GSH

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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: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 1.87→38.86 Å / Num. obs: 14913 / % possible obs: 96.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.026 / Rrim(I) all: 0.065 / Net I/σ(I): 14.4
Reflection shellResolution: 1.87→1.97 Å / Rmerge(I) obs: 0.648 / Num. unique obs: 3566 / CC1/2: 0.883 / Rpim(I) all: 0.279 / Rrim(I) all: 0.713

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HZE

8hze


Resolution: 1.87→28.16 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 755 5.06 %
Rwork0.2106 --
obs0.213 14913 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1551 61 85 1697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051794
X-RAY DIFFRACTIONf_angle_d1.032784
X-RAY DIFFRACTIONf_dihedral_angle_d11.399865
X-RAY DIFFRACTIONf_chiral_restr0.044359
X-RAY DIFFRACTIONf_plane_restr0.00880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-2.010.40481380.30862905X-RAY DIFFRACTION99
2.01-2.210.3281600.29022908X-RAY DIFFRACTION100
2.21-2.530.32561450.28992464X-RAY DIFFRACTION85
2.53-3.190.30821740.24542898X-RAY DIFFRACTION100
3.19-28.160.19131380.16162983X-RAY DIFFRACTION99

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