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- PDB-6k2i: Solution structure of camelid nanobody Nb11 against aflatoxin B1 -

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Basic information

Entry
Database: PDB / ID: 6k2i
TitleSolution structure of camelid nanobody Nb11 against aflatoxin B1
Componentscamelid nanobody Nb11
KeywordsAFB1-BINDING PROTEIN / Camelid antibody / Nanobody / Aflatoxin B1
Biological speciesVicugna pacos (alpaca)
MethodSOLUTION NMR / simulated annealing
AuthorsNie, Y. / Li, S.L. / He, T. / Zhu, J. / Yang, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21575155 China
CitationJournal: To Be Published
Title: Solution structure of camelid nanobody Nb11 against aflatoxin B1
Authors: Nie, Y. / Li, S.L. / He, T. / Zhu, J. / Yang, Y.H.
History
DepositionMay 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: camelid nanobody Nb11


Theoretical massNumber of molelcules
Total (without water)14,4811
Polymers14,4811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8290 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody camelid nanobody Nb11


Mass: 14481.106 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
161isotropic12D 1H-13C HSQC aromatic
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HNCA
171isotropic13D HN(CO)CA
181isotropic13D CBCA(CO)NH
191isotropic13D HN(CA)CB
1101isotropic13D HBHA(CO)NH
1111isotropic13D C(CO)NH
1121isotropic13D H(CCO)NH
1131isotropic13D (H)CCH-TOCSY
1141isotropic23D 1H-15N NOESY
1151isotropic23D 1H-13C NOESY aliphatic
1161isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-100% 13C; U-100% 15N] camelid nanobody 11, 90% H2O/10% D2O
Label: 13C,15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: camelid nanobody 11 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsDetails: 20 mM Tris-Hcl,150 mM NaCl,10% CH3OH,0.02% NaN3,10% D2O,pH=7.0,0.6 mM
Ionic strength: 0.15 M / Ionic strength err: 0.01 / Label: 13C,15N / pH: 7 / PH err: 0.01 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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