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- PDB-2m5a: Protein A binding by an engineered Affibody molecule -

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Basic information

Entry
Database: PDB / ID: 2m5a
TitleProtein A binding by an engineered Affibody molecule
Components
  • Immunoglobulin G-binding protein A
  • ZpA963
KeywordsPROTEIN BINDING / binding protein / protein engineering / protein A / Z domain / Affibody molecule
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
artificial gene (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHard, T.
CitationJournal: Protein Eng.Des.Sel. / Year: 2013
Title: High-affinity binding to staphylococcal protein A by an engineered dimeric Affibody molecule.
Authors: Lindborg, M. / Dubnovitsky, A. / Olesen, K. / Bjorkman, T. / Abrahmsen, L. / Feldwisch, J. / Hard, T.
History
DepositionFeb 19, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein A
B: ZpA963


Theoretical massNumber of molelcules
Total (without water)13,0422
Polymers13,0422
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area6840 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A


Mass: 6648.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Description: In-house standard expression vector with T7 promoter
Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P38507
#2: Protein ZpA963


Mass: 6394.071 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others)
Description: In-house standard expression vector with 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 HNCO
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D HN(COCA)CB
1613D 1H-15N TOCSY
1713D (H)CCH-COSY
1813D (H)CCH-TOCSY
1912D 1H-15N HSQC
11012D 1H-13C HSQC aliphatic
11112D (HB)CB(CGCDCE)HE
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11413D 1H-13C NOESY aromatic
11512D F1(13C,15N)-filtered, F2(13C)-edited NOESY
11623D HNCO
11723D HNCA
11823D HN(CO)CA
11923D HN(CA)CB
12023D HN(COCA)CB
12123D 1H-15N TOCSY
12223D (H)CCH-COSY
12323D (H)CCH-TOCSY
12422D 1H-15N HSQC
12522D 1H-13C HSQC aliphatic
12622D (HB)CB(CGCDCE)HE
12723D 1H-15N NOESY
12823D 1H-13C NOESY aliphatic
12923D 1H-13C NOESY aromatic
13022D F1(13C,15N)-filtered, F2(13C)-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 to 1 mM [U-99% 13C; U-99% 15N] Z domain, 25% molar excess mM ZpA963, 93% H2O/7% D2O93% H2O/7% D2O
20.5 to 1.0 mM [U-99% 13C; U-99% 15N] ZpA963, 25 5 molar excess mM Z domain, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMZ domain-1[U-99% 13C; U-99% 15N]1
0.25 mMZpA963-21
0.5 mMZpA963-3[U-99% 13C; U-99% 15N]2
0.25 mMZ domain-42
Sample conditionsIonic strength: 0.095 / pH: 5.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcPNMRCCPNpeak picking
CcPNMRCCPNchemical shift assignment
CcPNMRCCPNdata analysis
DANGLECheung MS, Maguire ML, Stevens TJ & Broadhurst RW (2010) J Magn Reson 202, 223-233.data analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 50 / Conformers submitted total number: 20

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