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- PDB-1ieh: SOLUTION STRUCTURE OF A SOLUBLE SINGLE-DOMAIN ANTIBODY WITH HYDRO... -

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Basic information

Entry
Database: PDB / ID: 1ieh
TitleSOLUTION STRUCTURE OF A SOLUBLE SINGLE-DOMAIN ANTIBODY WITH HYDROPHOBIC RESIDUES TYPICAL OF A VL/VH INTERFACE
ComponentsBRUC.D4.4
KeywordsIMMUNE SYSTEM / two pleated beta-sheet / immunoglobulin beta-barrel
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodSOLUTION NMR / simulated annealing using torsion angle, cartesian dynamics
AuthorsVranken, W. / Tolkatchev, D. / Xu, P. / Tanha, J. / Chen, Z. / Narang, S. / Ni, F.
CitationJournal: Biochemistry / Year: 2002
Title: Solution structure of a llama single-domain antibody with hydrophobic residues typical of the VH/VL interface.
Authors: Vranken, W. / Tolkatchev, D. / Xu, P. / Tanha, J. / Chen, Z. / Narang, S. / Ni, F.
History
DepositionApr 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRUC.D4.4


Theoretical massNumber of molelcules
Total (without water)14,6181
Polymers14,6181
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)10 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody BRUC.D4.4


Mass: 14618.006 Da / Num. of mol.: 1 / Fragment: SINGLE DOMAIN ANTIBODY FROM A NAIVE LLAMA LIBRARY
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D combined 13C/15N-separated NOESY

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Sample preparation

DetailsContents: 10mM sodium phosphate 150mM NaCl 0.2mM EDTA / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.16 / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeFrank Delaglio, Stephan Grzesiek, Ad Bax, Geerten W. Vuister, Guang Zhu, John Pfeiferprocessing
NMRView4.1.2Bruce Johnson and Richard Blevinsdata analysis
ARIA1J. Linge and M. Nilgesstructure solution
CNS1AT Brunger, PD Adams, GM Clore, WL DeLano, P Gros, RW Grosse-Kunstleve, JS Jiang, J Kuszewski, M Nilges, NS Pannu, RJ Read, LM Rice, T Simonson, GL Warrenstructure solution
ARIA1Linge, Nilgesrefinement
RefinementMethod: simulated annealing using torsion angle, cartesian dynamics
Software ordinal: 1
Details: NO MANUAL ASSIGNMENTS OF NOE PEAKS WERE INITIALLY PERFORMED - THE GLOBAL FOLD OF THE PROTEIN WAS DETERMINED USING RESTRAINTS WITH LOW AMBIGUITY. THE SET OF GLOBAL FOLD STRUCTURES SERVED AS ...Details: NO MANUAL ASSIGNMENTS OF NOE PEAKS WERE INITIALLY PERFORMED - THE GLOBAL FOLD OF THE PROTEIN WAS DETERMINED USING RESTRAINTS WITH LOW AMBIGUITY. THE SET OF GLOBAL FOLD STRUCTURES SERVED AS AN ASSIGNMENT FILTER TO REDUCE THE AMBIGUITY OF THE OTHER RESTRAINTS. THE RESTRAINT LIST AND STRUCTURES WERE FURTHER REFINED BY MANUALLY CHOOSING POSSIBILITIES FROM THE RESTRAINTS WITH LOW AMBIGUITY (BASED ON THE SPECTRA).
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 10

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