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- PDB-7eoi: Crystal structure of the Pepper aptamer in complex with HBC, mang... -

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Basic information

Entry
Database: PDB / ID: 7eoi
TitleCrystal structure of the Pepper aptamer in complex with HBC, manganese soak
ComponentsPepper (49-MER)
KeywordsRNA / Fluorescent RNA / Aptamer / HBC
Function / homologyChem-J8F / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsHuang, K.Y. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Structure-based investigation of fluorogenic Pepper aptamer.
Authors: Huang, K. / Chen, X. / Li, C. / Song, Q. / Li, H. / Zhu, L. / Yang, Y. / Ren, A.
History
DepositionApr 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,45510
Polymers15,7731
Non-polymers6829
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.619, 34.702, 54.141
Angle α, β, γ (deg.)90.000, 122.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain Pepper (49-MER)


Mass: 15773.372 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: Chemical ChemComp-J8F / 4-[(~{Z})-1-cyano-2-[4-[2-hydroxyethyl(methyl)amino]phenyl]ethenyl]benzenecarbonitrile


Mass: 303.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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

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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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium chloride, 0.005 M magnesium chloride, 0.025 M HEPES, pH 7.0, 1.25 M 1,6-hexanediol, 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.192 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: 1.192 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 15509 / % possible obs: 77.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.073 / Rrim(I) all: 0.188 / Χ2: 2.054 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.972.80.5532080.7570.3260.6480.66319.3
1.97-2.053.20.5814880.6350.3210.670.68545.6
2.05-2.1440.5476220.7770.2730.6150.65958.7
2.14-2.254.50.577410.7920.2740.6360.76468.2
2.25-2.395.40.4259320.850.1880.4670.79887
2.39-2.586.10.37610620.9280.1630.4110.70997.9
2.58-2.846.40.26110510.9580.1090.2830.83797.8
2.84-3.256.70.17110710.9760.0710.1851.49598.9
3.25-4.096.70.14610670.9790.060.1582.42298.1
4.09-506.50.15711220.7760.0660.176.63998.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EOG

7eog


Resolution: 1.92→35.993 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 711 4.58 %
Rwork0.2152 14798 -
obs0.2166 15509 77.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.97 Å2 / Biso mean: 42.0224 Å2 / Biso min: 18.73 Å2
Refinement stepCycle: final / Resolution: 1.92→35.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1045 31 85 1161
Biso mean--35.14 33.25 -
Num. residues----49
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-2.06810.3531640.2817136436
2.0681-2.27620.2661280.305235362
2.2762-2.60550.3261520.2745355492
2.6055-3.28230.29291700.2374376998
3.2823-35.9930.20021970.1771375898

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