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- PDB-7eol: Crystal structure of the Pepper aptamer in complex with HBC497 -

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Basic information

Entry
Database: PDB / ID: 7eol
TitleCrystal structure of the Pepper aptamer in complex with HBC497
ComponentsPepper (49-MER)
KeywordsRNA / Fluorescent RNA / Aptamer / HBC497
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / Chem-J8O / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.309 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)16,3788
Polymers15,4281
Non-polymers9507
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-9 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.676, 34.782, 57.909
Angle α, β, γ (deg.)90.000, 127.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain Pepper (49-MER)


Mass: 15428.166 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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#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: Chemical ChemComp-J8O / 4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]pyrazin-2-yl]ethenyl]benzenecarbonitrile


Mass: 305.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N5O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
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: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 6446 / % possible obs: 98.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.063 / Rrim(I) all: 0.16 / Χ2: 1.588 / Net I/σ(I): 5 / Num. measured all: 41036
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.386.50.3826360.8870.1620.4160.99499.7
2.38-2.486.40.3386460.930.1450.3690.94999.4
2.48-2.596.40.3076350.9410.130.3351.06398.8
2.59-2.736.20.2536360.9580.1090.2761.22199.4
2.73-2.96.20.2056510.9710.0890.2241.52597.9
2.9-3.126.60.1666320.980.0710.1811.83199.7
3.12-3.446.60.1446390.9810.0620.1572.06598.9
3.44-3.936.30.1366430.9830.060.1492.05498.6
3.93-4.956.30.1316600.9810.0560.1432.08598.4
4.95-506.20.1136680.9890.0490.1242.07797.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EOG

7eog


Resolution: 2.309→31.429 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 34.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 315 4.9 %
Rwork0.2187 6116 -
obs0.2212 6431 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.92 Å2 / Biso mean: 40.377 Å2 / Biso min: 13.12 Å2
Refinement stepCycle: final / Resolution: 2.309→31.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1054 28 60 1142
Biso mean--28.62 29.81 -
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 (%)
2.309-2.90860.31771640.2529299496
2.9086-31.4290.24761510.2075312298

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