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- PDB-6sow: NMR solution structure of staphylococcal protein A, C domain -

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Basic information

Entry
Database: PDB / ID: 6sow
TitleNMR solution structure of staphylococcal protein A, C domain
ComponentsImmunoglobulin G binding protein A
KeywordsPROTEIN BINDING / three-helix bundle / immunoglobulin-binding protein / immune system
Function / homology
Function and homology information


IgG binding / immunoglobulin binding / : / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily ...Octapeptide repeat / Octapeptide repeat / 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
Similarity search - Domain/homology
Immunoglobulin G-binding protein A / Immunoglobulin G binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsBacklund, S.M. / Iwai, H.
Funding support Finland, 3items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
Academy of Finland137995 Finland
Academy of Finland131413 Finland
CitationJournal: Molecules / Year: 2021
Title: NMR Structure Determinations of Small Proteins Using only One Fractionally 20% 13 C- and Uniformly 100% 15 N-Labeled Sample.
Authors: Heikkinen, H.A. / Backlund, S.M. / Iwai, H.
History
DepositionAug 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G binding protein A


Theoretical massNumber of molelcules
Total (without water)6,6531
Polymers6,6531
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4540 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G binding protein A


Mass: 6653.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UW48, UniProt: P02976*PLUS

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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
131isotropic13D HNCA
1101isotropic13D HNCACBi
1111isotropic13D HNCO
1121isotropic13D HNCOi
1131isotropic12D CACO
1141isotropic12D CON
1151isotropic13D (H)CCH-COSY
292isotropic12D 1H-15N HSQC
222isotropic12D 1H-13C HSQC
1162isotropic12D 1H-13C HSQC aromatic
242isotropic12D CACO
252isotropic12D CON
262isotropic13D (H)CCH-COSY
272isotropic13D 1H-15N NOESY
282isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution15.6 mM [U-20% 13C; U-100% 15N] Protein A C domain, 95% H2O/5% D2Osample_195% H2O/5% D2O
solution22.8 mM [U-20% 13C; U-100% 15N] Protein A C domain, 95% H2O/5% D2Osample_295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5.6 mMProtein A C domain[U-20% 13C; U-100% 15N]1
2.8 mMProtein A C domain[U-20% 13C; U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mMconditions_16 1 atm303 K
220 mMconditions_26 1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CcpNmr Analysis2.4.2CCPNpeak picking
PSVS1.5Bhattacharya and Montelionedata analysis
TALOSNCornilescu, Delaglio and Baxchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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