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- PDB-7eok: Crystal structure of the Pepper aptamer in complex with HBC485 -

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Basic information

Entry
Database: PDB / ID: 7eok
TitleCrystal structure of the Pepper aptamer in complex with HBC485
ComponentsPepper (49-MER)
KeywordsRNA / Fluorescent RNA / Aptamer / HBC485
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / Chem-J8L / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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)16,50212
Polymers15,4281
Non-polymers1,07411
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-11 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.982, 37.720, 56.740
Angle α, β, γ (deg.)90.000, 127.080, 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-J8L / 4-[(~{Z})-1-cyano-2-[5-[2-(dimethylamino)ethyl-methyl-amino]pyrazin-2-yl]ethenyl]benzenecarbonitrile


Mass: 332.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
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: 1.102 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: 1.102 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 4422 / % possible obs: 97.3 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.069 / Rrim(I) all: 0.163 / Χ2: 1.164 / Net I/σ(I): 4.3 / Num. measured all: 22403
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.83.30.6614180.7710.3880.7720.60892.5
2.8-2.913.80.5934150.920.3340.6850.62996.3
2.91-3.044.40.3924470.9710.2040.4440.80198.5
3.04-3.24.70.34450.9820.1510.3370.93497.4
3.2-3.45.10.254550.9890.1180.2771.2298.5
3.4-3.665.30.2084200.9870.0990.2311.26595.2
3.66-4.0360.24430.9890.0910.2211.32699.1
4.03-4.626.20.1674620.9850.0720.1821.21499.6
4.62-5.815.80.1244380.990.0570.1371.27397.8
5.81-505.80.0884790.9940.0420.0981.62897.8

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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: 2.7→45.222 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 228 5.28 %
Rwork0.2019 4091 -
obs0.2039 4319 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.48 Å2 / Biso mean: 64.0061 Å2 / Biso min: 19.89 Å2
Refinement stepCycle: final / Resolution: 2.7→45.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1054 34 21 1109
Biso mean--58.75 47.59 -
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 (%)
2.7-3.40160.30391160.2584201396
3.4016-45.2220.21681120.1825207897

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