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- PDB-7eoh: Crystal structure of the Pepper aptamer in complex with HBC -

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Basic information

Entry
Database: PDB / ID: 7eoh
TitleCrystal structure of the Pepper aptamer in complex with HBC
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: 1.637 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)16,2787
Polymers15,8531
Non-polymers4256
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-9 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.642, 35.023, 58.127
Angle α, β, γ (deg.)90.000, 127.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-288-

HOH

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Components

#1: RNA chain Pepper (49-MER)


Mass: 15853.353 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.637→50 Å / Num. obs: 17900 / % possible obs: 98.3 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.058 / Rrim(I) all: 0.146 / Χ2: 1.539 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.64-1.74.60.6416380.9180.2990.710.65991.2
1.7-1.775.20.62617380.9160.2830.6890.69796.4
1.77-1.855.70.58917910.8620.2640.6470.76998.8
1.85-1.946.20.48717820.8950.2090.5310.8899.1
1.94-2.076.70.38118320.9340.1580.4131.081100
2.07-2.236.70.30917820.9410.1280.3351.29699.9
2.23-2.456.40.2317990.970.0990.2511.65299.3
2.45-2.86.90.17418370.9830.0720.1881.98999.8
2.8-3.536.30.11718250.990.0510.1282.81999
3.53-506.50.10218760.9860.0450.1112.80399.4

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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: 1.637→36.561 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 915 5.12 %
Rwork0.1974 16944 -
obs0.1993 17859 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.98 Å2 / Biso mean: 39.0723 Å2 / Biso min: 14.74 Å2
Refinement stepCycle: final / Resolution: 1.637→36.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1050 28 144 1222
Biso mean--28.94 35.3 -
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 (%)
1.637-1.72330.32281120.2958208884
1.7233-1.83130.29511160.2551242898
1.8313-1.97270.24071350.2306243599
1.9727-2.17120.26251270.20892494100
2.1712-2.48530.2821320.2162247999
2.4853-3.1310.2461510.21592482100
3.131-36.5610.19651420.1657253899

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