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- PDB-9gv4: TBA G-quadruplex binding nanobody (free form) -

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Basic information

Entry
Database: PDB / ID: 9gv4
TitleTBA G-quadruplex binding nanobody (free form)
ComponentsNanobody
KeywordsIMMUNE SYSTEM / Nanobody / G-quadruplex / TBA / thrombin / DNA
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.534 Å
AuthorsPevec, M. / Hadzi, S.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyJ1-50026 Slovenia
Slovenian Research AgencyP1-0201 Slovenia
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural basis of G-quadruplex recognition by a camelid antibody fragment.
Authors: Pevec, M. / Medved, T. / Kovacic, M. / Zerjav, N. / Imperl, J. / Plavec, J. / Lah, J. / Loris, R. / Hadzi, S.
History
DepositionSep 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1519
Polymers13,4251
Non-polymers7278
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-48 kcal/mol
Surface area6870 Å2
Unit cell
Length a, b, c (Å)24.125, 84.257, 97.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-204-

SO4

21A-312-

HOH

31A-345-

HOH

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Components

#1: Antibody Nanobody


Mass: 13424.901 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pHEN6c / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.67 Å3/Da / Density % sol: 26.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: 1.6 M Ammonium sulphate 0.1 M HEPES, pH=7.25 cryoprotection=25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.53→48.721 Å / Num. obs: 15415 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Χ2: 0.96 / Net I/σ(I): 16.1
Reflection shellResolution: 1.53→1.57 Å / % possible obs: 98.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.441 / Num. measured all: 7056 / Num. unique obs: 1099 / CC1/2: 0.931 / Rpim(I) all: 0.188 / Rrim(I) all: 0.48 / Χ2: 0.93 / Net I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.534→48.721 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 1539 10.01 %
Rwork0.1699 --
obs0.1732 15380 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.534→48.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 41 126 1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071036
X-RAY DIFFRACTIONf_angle_d0.9411409
X-RAY DIFFRACTIONf_dihedral_angle_d16.314604
X-RAY DIFFRACTIONf_chiral_restr0.054143
X-RAY DIFFRACTIONf_plane_restr0.004182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.534-1.58330.39721340.33391212X-RAY DIFFRACTION98
1.5833-1.63990.40621380.30211236X-RAY DIFFRACTION100
1.6399-1.70560.30031380.25771238X-RAY DIFFRACTION100
1.7056-1.78320.26681370.21131233X-RAY DIFFRACTION100
1.7832-1.87720.22971390.17941249X-RAY DIFFRACTION100
1.8772-1.99490.18191400.17721260X-RAY DIFFRACTION100
1.9949-2.14890.21341360.15531236X-RAY DIFFRACTION100
2.1489-2.36510.19711410.16141258X-RAY DIFFRACTION100
2.3651-2.70740.19381420.16531275X-RAY DIFFRACTION100
2.7074-3.41090.18181430.13811283X-RAY DIFFRACTION100
3.4109-48.7210.14811510.1381361X-RAY DIFFRACTION100

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