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- PDB-2lr2: Designed IgG and lanthanide binding probe for solution NMR, MRI a... -

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Basic information

Entry
Database: PDB / ID: 2lr2
TitleDesigned IgG and lanthanide binding probe for solution NMR, MRI and luminescence microscopy
ComponentsImmunoglobulin G-binding protein A
KeywordsDE NOVO PROTEIN / z domain / lanthanide binding tag
Function / homologyImmunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesartificial gene (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBarb, A.W. / Ho, T.G. / Prestegard, J.H.
CitationJournal: Protein Sci. / Year: 2012
Title: Lanthanide binding and IgG affinity construct: Potential applications in solution NMR, MRI, and luminescence microscopy.
Authors: Barb, A.W. / Ho, T.G. / Flanagan-Steet, H. / Prestegard, J.H.
History
DepositionMar 21, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)9,8761
Polymers9,8761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G-binding protein A


Mass: 9875.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
Compound detailsTHE AUTHORS STATE THAT THE THREE HELICES ARE FROM THE Z DOMAIN WHICH IS A DERIVATIVE OF THE B ...THE AUTHORS STATE THAT THE THREE HELICES ARE FROM THE Z DOMAIN WHICH IS A DERIVATIVE OF THE B DOMAIN FROM THE STAPHYLOCOCCUS AUREUS POLYPEPTIDE CALLED PROTEIN A.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This entry details the top 2 models from an xplor simulation to satisfy the orientation of a lanthanide-binding domain with the underlying Protein A-derived Z domain using paramagnetic NMR ...Details: This entry details the top 2 models from an xplor simulation to satisfy the orientation of a lanthanide-binding domain with the underlying Protein A-derived Z domain using paramagnetic NMR constraints. There is no explicit information regarding the placement of the domain-connecting loops, but these were included in the calculation and are presented to demonstrate the potential covalent restriction of the lanthanide-binding tag portion of the chimeric protein.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D HN(COCA)CB

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Sample preparation

DetailsContents: 100-800 uM [U-98% 13C; U-98% 15N] Z-L2LBT, 90 % H2O, 10 % [U-2H] D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMZ-L2LBT-1[U-98% 13C; U-98% 15N]100-8001
90 %H2O-21
10 %D2O-3[U-2H]1
Sample conditionsIonic strength: 0.1 / pH: 8 / Pressure: ambient / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS9001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: dihedral, PRE and PCS constraints used.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 2

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