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- PDB-2jvg: Structure of C3-binding domain 4 of Staphylococcus aureus protein Sbi -

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Basic information

Entry
Database: PDB / ID: 2jvg
TitleStructure of C3-binding domain 4 of Staphylococcus aureus protein Sbi
ComponentsIgG-binding protein SBI
KeywordsIMMUNE SYSTEM / three helix bundle
Function / homology
Function and homology information


IgG binding / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin-binding protein Sbi, domain IV / C3 binding domain 4 of IgG-bind protein SBI / Sbi, C3 binding domain IV / Sbi, C3 binding domain IV / Protein A, Ig-binding domain / B domain / Immunoglobulin/albumin-binding domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin-binding protein Sbi / Immunoglobulin-binding protein Sbi
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsStructure of Sbi domain 4. NMR-derived ensemble of twenty structures.
AuthorsUpadhyay, A. / Burman, J. / Clark, E.A. / van den Elsen, J.M.H. / Bagby, S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure-function analysis of the C3 binding region of Staphylococcus aureus immune subversion protein Sbi.
Authors: Upadhyay, A. / Burman, J.D. / Clark, E.A. / Leung, E. / Isenman, D.E. / van den Elsen, J.M. / Bagby, S.
History
DepositionSep 20, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IgG-binding protein SBI


Theoretical massNumber of molelcules
Total (without water)8,1231
Polymers8,1231
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)20 / 50structures with the lowest energy
RepresentativeModel #1rmsd from average + energy

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Components

#1: Protein IgG-binding protein SBI


Mass: 8123.308 Da / Num. of mol.: 1 / Fragment: UNP residues 198-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sbi / Production host: Escherichia coli (E. coli) / References: UniProt: Q99RL2, UniProt: Q931F4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of Sbi domain 4. NMR-derived ensemble of twenty structures.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1413D HNHA
1523D CBCA(CO)NH
1623D HN(CA)CB
1723D HNCO
1823D HN(CA)CO
1923D C(CO)NH
11023D H(CCO)NH
11123D (H)CCH-TOCSY
11223D HBHA(CO)NH
11323D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
15 mM MES, 100 mM sodium chloride, 1 mM EDTA, 1 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
25 mM MES, 100 mM sodium chloride, 1 mM EDTA, 1 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
5 mMMES1
100 mMsodium chloride1
1 mMEDTA1
1 mMbenzamidine1
5 mMMES2
100 mMsodium chloride2
1 mMEDTA2
1 mMbenzamidine2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1025.5ambient 289 K
20.1025.5ambient 289 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AnalysisCCPNdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
ProcheckNMRLaskowski and MacArthurstructure solution
ProcheckNMRLaskowski and MacArthurrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: refine.py in Xplor-NIH
NMR representativeSelection criteria: rmsd from average + energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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