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- PDB-7eop: Crystal structure of the Pepper aptamer in complex with HBC620 -

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Basic information

Entry
Database: PDB / ID: 7eop
TitleCrystal structure of the Pepper aptamer in complex with HBC620
ComponentsPepper (49-MER)
KeywordsRNA / Fluorescent RNA / Aptamer / HBC620
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / Chem-J93 / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)16,4388
Polymers15,4281
Non-polymers1,0107
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-9 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.447, 34.983, 57.839
Angle α, β, γ (deg.)90.000, 127.570, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-295-

HOH

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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 / Guanosine 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-J93 / 4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]thieno[3,2-b]thiophen-2-yl]ethenyl]benzenecarbonitrile


Mass: 365.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15N3OS2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
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: May 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 13710 / % possible obs: 99.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Χ2: 0.502 / Net I/σ(I): 3.7 / Num. measured all: 89200
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.865.80.6413330.8160.2850.7030.43997.4
1.86-1.946.30.54313740.8550.2350.5930.4699.5
1.94-2.036.60.44913450.920.1880.4870.46999.9
2.03-2.136.70.34513710.9430.1440.3740.4999.7
2.13-2.276.10.26813310.9590.1160.2930.48497
2.27-2.4470.19913740.9820.0810.2150.52999.9
2.44-2.696.90.14813900.9880.060.160.53299.9
2.69-3.086.50.08413770.9960.0350.0920.59999.6
3.08-3.886.60.05113880.9980.0210.0550.57799
3.88-506.50.04114270.9980.0170.0440.42199.4

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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: 1.8→28.914 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 656 4.79 %
Rwork0.19 13035 -
obs0.1911 13691 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.17 Å2 / Biso mean: 34.5877 Å2 / Biso min: 8.33 Å2
Refinement stepCycle: final / Resolution: 1.8→28.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1054 30 151 1235
Biso mean--25.9 29.73 -
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 (%)
1.8-1.9390.29371060.2304259098
1.939-2.13410.24031530.20592558100
2.1341-2.44270.24461280.2059258098
2.4427-3.0770.23961330.20392632100
3.077-28.9140.17361360.169267599

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