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- PDB-6iyn: Solution structure of camelid nanobody Nb26 against aflatoxin B1 -

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Basic information

Entry
Database: PDB / ID: 6iyn
TitleSolution structure of camelid nanobody Nb26 against aflatoxin B1
ComponentsNb26
KeywordsAFLATOXIN B1-BINDING PROTEIN / Camelid antibody / Nanobody / Aflatoxin B1
Biological speciesVicugna pacos (alpaca)
MethodSOLUTION NMR / molecular dynamics
AuthorsNie, Y. / He, T. / Zhu, J. / Li, S.L. / Hu, R. / Yang, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21575155 China
CitationJournal: Biomol NMR Assign / Year: 2019
Title: Chemical shift assignments of a camelid nanobody against aflatoxin B1.
Authors: Nie, Y. / Li, S. / Zhu, J. / Hu, R. / Liu, M. / He, T. / Yang, Y.
History
DepositionDec 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 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:
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Assembly

Deposited unit
A: Nb26


Theoretical massNumber of molelcules
Total (without water)14,5271
Polymers14,5271
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7940 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 Nb26


Mass: 14527.089 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 aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CO
1111isotropic13D HNCA
1101isotropic13D HN(CA)CO
191isotropic13D CBCA(CO)NH
181isotropic13D HN(CA)CB
171isotropic13D HBHA(CO)NH
161isotropic13D C(CO)NH
1181isotropic13D H(CCO)NH
1171isotropic13D (H)CCH-TOCSY
2252isotropic23D 1H-15N NOESY
2242isotropic23D 1H-13C NOESY aliphatic
2532isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.45 mM [U-100% 13C; U-100% 15N] camelid nanobody 26, 90% H2O/10% D2O13C,15N90% H2O/10% D2O
solution20.55 mM [U-100% 13C; U-100% 15N] camelid nanobody 26, 90% H2O/10% D2O13C,15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.45 mMcamelid nanobody 26[U-100% 13C; U-100% 15N]1
0.55 mMcamelid nanobody 26[U-100% 13C; U-100% 15N]2
Sample conditions

Ionic strength: 0.15 M / Ionic strength err: 0.01 / Label: 13C,15N / pH: 7.0 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

Conditions-IDDetails
120 mM Tris-HCl,150 mM NaCl,10%CH3OH,0.02% NaN3,10% D2O,pH=7.0,0.5 mM
220 mM Tris-HCl,150 mM NaCl,10%CH3OH,0.02% NaN3,10% D2O,pH=7.0,0.55 mM

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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: molecular dynamics / Software ordinal: 1
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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