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- PDB-2spz: STAPHYLOCOCCAL PROTEIN A, Z-DOMAIN, NMR, 10 STRUCTURES -

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Entry
Database: PDB / ID: 2spz
TitleSTAPHYLOCOCCAL PROTEIN A, Z-DOMAIN, NMR, 10 STRUCTURES
ComponentsIMMUNOGLOBULIN G BINDING PROTEIN A
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN-BINDING PROTEIN / THREE-HELICAL BUNDLE STRUCTURE
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 / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / 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 / 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 / SIMULATED ANNEALING WITH RESTRAINED MOLECULAR DYNAMICS
AuthorsMontelione, G.T. / Tashiro, M. / Tejero, R. / Lyons, B.A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: High-resolution solution NMR structure of the Z domain of staphylococcal protein A.
Authors: Tashiro, M. / Tejero, R. / Zimmerman, D.E. / Celda, B. / Nilsson, B. / Montelione, G.T.
#1: Journal: Biochemistry / Year: 1996
Title: The Mechanism of Binding Staphylococcal Protein a to Immunoglobin G Does not Involve Helix Unwinding
Authors: Jendeberg, L. / Tashiro, M. / Tejero, R. / Lyons, B.A. / Uhlen, M. / Montelione, G.T. / Nilsson, B.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1995
Title: Structures of Bacterial Immunoglobulin-Binding Domains and Their Complexes with Immunoglobulin
Authors: Tashiro, M. / Montelione, G.T.
#3: Journal: Biochemistry / Year: 1993
Title: An Improved Strategy for Determining Resonance Assignments for Isotopically Enriched Proteins and its Application to an Engineered Domain of Staphylococcal Protein A
Authors: Lyons, B.A. / Tashiro, M. / Cedergren, L. / Nilsson, B. / Montelione, G.T.
History
DepositionJul 29, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 5, 1998Provider: repository / Type: Initial release
SupersessionApr 21, 2000ID: 1SPZ
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMMUNOGLOBULIN G BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)6,6481
Polymers6,6481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40LOWEST CONFORMATIONAL ENERGY
RepresentativeModel #1

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Components

#1: Antibody IMMUNOGLOBULIN G BINDING PROTEIN A


Mass: 6648.316 Da / Num. of mol.: 1 / Fragment: Z DOMAIN / Mutation: A1V, G29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Cellular location: CELL WALL / Plasmid: PDHZ / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 / References: UniProt: P38507

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE REMARKS
NMR detailsText: NULL NMR EXPERIMENTS CONDUCTED: 2D PFG-[15N]HSQC, 3D PFG-HNCO, 3D PFG-(HA)CA(CO)NH, 3D PFG-HA(CA)(CO)NH, 3D PFG-HA(CA)NH, 3D PFG-CBCANH, 3D PFG-CBCA(CO)NH, 3D PFG- (HA)CANH, 3D PFG-HN(CA)CO, 3D ...Text: NULL NMR EXPERIMENTS CONDUCTED: 2D PFG-[15N]HSQC, 3D PFG-HNCO, 3D PFG-(HA)CA(CO)NH, 3D PFG-HA(CA)(CO)NH, 3D PFG-HA(CA)NH, 3D PFG-CBCANH, 3D PFG-CBCA(CO)NH, 3D PFG- (HA)CANH, 3D PFG-HN(CA)CO, 3D PFG-HCCNH-TOCSY, 3D PFG-HCC (CO)NH-TOCSY, 2D CT

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Sample preparation

Sample conditionsIonic strength: 10 MILLIMOLAR K2HPO4 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian MODIFIED UNITY 500 / Manufacturer: Varian / Model: MODIFIED UNITY 500 / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CONGENBRUCCOLERI,KARPLUSrefinement
DIANAstructure solution
CONGENstructure solution
RefinementMethod: SIMULATED ANNEALING WITH RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST CONFORMATIONAL ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 10

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