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- PDB-2kzi: Solution structure of the ZHER2 Affibody -

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Basic information

Entry
Database: PDB / ID: 2kzi
TitleSolution structure of the ZHER2 Affibody
ComponentsEngineered protein, ZHER2 Affibody
KeywordsPROTEIN BINDING / engineered protein
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 speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsarbitrary, model 1
AuthorsHard, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for high-affinity HER2 receptor binding by an engineered protein.
Authors: Eigenbrot, C. / Ultsch, M. / Dubnovitsky, A. / Abrahmsen, L. / Hard, T.
History
DepositionJun 18, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engineered protein, ZHER2 Affibody


Theoretical massNumber of molelcules
Total (without water)8,1471
Polymers8,1471
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)22 / 50structures with the lowest energy
RepresentativeModel #1arbitrary

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Components

#1: Protein Engineered protein, ZHER2 Affibody


Mass: 8147.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Description: pET derived, T7 promoter / 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-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] ZHER2 affibody-1, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: ZHER2 affibody-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.18 / pH: 6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPNMRDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: arbitrary
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 22

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