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- PDB-1edl: STAPHYLOCOCCAL PROTEIN A E-DOMAIN (-60), NMR, 22 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1edl
TitleSTAPHYLOCOCCAL PROTEIN A E-DOMAIN (-60), NMR, 22 STRUCTURES
ComponentsSTAPHYLOCOCCAL PROTEIN A
KeywordsIMMUNOGLOBULIN-BINDING PROTEIN / TRANSMEMBRANE / CELL WALL / IGG-BINDING PROTEIN
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / LysM domain superfamily / Lysin motif / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / LysM domain superfamily / Lysin motif / 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)
MethodSOLUTION NMR / DG, RESTRAINED MOLECULAR DYNAMICS
AuthorsStarovasnik, M.A. / Skelton, N.J. / Fairbrother, W.J.
CitationJournal: Biochemistry / Year: 1996
Title: Solution structure of the E-domain of staphylococcal protein A.
Authors: Starovasnik, M.A. / Skelton, N.J. / O'Connell, M.P. / Kelley, R.F. / Reilly, D. / Fairbrother, W.J.
History
DepositionJul 22, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STAPHYLOCOCCAL PROTEIN A


Theoretical massNumber of molelcules
Total (without water)6,2041
Polymers6,2041
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 / 50LOWEST RESTRAINT VIOLATION ENERGY
Representative

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Components

#1: Protein STAPHYLOCOCCAL PROTEIN A


Mass: 6203.667 Da / Num. of mol.: 1 / Fragment: E-DOMAIN
Source method: isolated from a genetically manipulated source
Details: PHE 11 CHI 1 ROTOMER IS -60 DEGREES / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P38507

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D COSY
121TOCSY
131NOESY
1412Q
151COSY-35
161HSQC
171TOCSY-HSQC

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Sample preparation

Sample conditionspH: 5.7 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 500 / Manufacturer: Bruker / Model: AMX 500 / Field strength: 500 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionDeveloperClassification
DiscoverBIOSYMrefinement
DGIIstructure solution
DISCOVER (BIOSYM)(BIOSYM)structure solution
RefinementMethod: DG, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST RESTRAINT VIOLATION ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 20

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