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- PDB-1bdd: STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN,... -

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Basic information

Entry
Database: PDB / ID: 1bdd
TitleSTAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsSTAPHYLOCOCCUS AUREUS PROTEIN A
KeywordsIMMUNOGLOBULIN-BINDING PROTEIN / TRANSMEMBRANE / CELL WALL / IMMUNOGLOBULIN BINDING DOMAIN
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 / HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD
AuthorsGouda, H. / Torigoe, H. / Saito, A. / Sato, M. / Arata, Y. / Shimada, I.
Citation
Journal: Biochemistry / Year: 1992
Title: Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.
Authors: Gouda, H. / Torigoe, H. / Saito, A. / Sato, M. / Arata, Y. / Shimada, I.
#1: Journal: FEBS Lett. / Year: 1990
Title: 15N Nuclear Magnetic Resonance Studies of the B Domain of Staphylococcal Protein A: Sequence Specific Assignments of the Imide 15N Resonances of the Proline Residues and the Interaction with Human Immunoglobulin G
Authors: Torigoe, H. / Shimada, I. / Waelchli, M. / Saito, A. / Sato, M. / Arata, Y.
#2: Journal: Biochemistry / Year: 1990
Title: Sequential 1H NMR Assignments and Secondary Structure of the B Domain of Staphylococcal Protein A: Structural Changes between the Free B Domain in Solution and the Fc-Bound B Domain in Crystal
Authors: Torigoe, H. / Shimada, I. / Saito, A. / Sato, M. / Arata, Y.
#3: Journal: Protein Eng. / Year: 1989
Title: High Level Expression of a Synthetic Gene Coding for Igg-Binding Domain B of Staphylococcal Protein A
Authors: Saito, A. / Honda, S. / Nishi, T. / Koike, M. / Okazaki, K. / Itoh, S. / Sato, M.
History
DepositionJun 28, 1996Processing site: BNL
Revision 1.0Jan 11, 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: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: STAPHYLOCOCCUS AUREUS PROTEIN A


Theoretical massNumber of molelcules
Total (without water)6,7781
Polymers6,7781
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)1 / 55AT FIRST, THE DEPOSITORS CARRIED OUT THE DISTANCE GEOMETRY CALCULATION BY STARTING FROM 55 INITIAL STRUCTURES. THIS CALCULATION RESULTED IN 41 SOLUTIONS, WHICH HAD CORRECT POLYPEPTIDE FOLDS EXCLUDING 14 MIRROR-IMAGE SUBSTRUCTURES. NEXT, THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS WERE PERFORMED BY USING THESE 41 SUBSTRUCTURES. THE DISTANCE AND TORSION ANGLE VIOLATIONS OF THE 41 SOLUTIONS OBTAINED BY THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS WERE SMALLER THAN 0.6 ANGSTROMS AND 27 DEGREES, RESPECTIVELY. THE DEPOSITORS SELECTED 10 SOLUTIONS THAT HAD THE DISTANCE AND TORSION ANGLE VIOLATIONS OF SMALLER THAN 0.5 ANGSTROMS AND 10 DEGREES, RESPECTIVELY.
Representative

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Components

#1: Protein STAPHYLOCOCCUS AUREUS PROTEIN A


Mass: 6778.418 Da / Num. of mol.: 1 / Fragment: B DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SYNTHETIC GENE / Plasmid: PPRAFW1 / 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
111DQF-COSY
121HOHAHA
131NOESY
141PE-COSY; 1H-15N HSQC
151DOUBLE-DEPT
1612D-HMQC-HOHAHA
1712D-HMQC-NOESY
181HMQC-J

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Sample preparation

Sample conditionspH: 5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: JEOL JNM GSX / Manufacturer: JEOL / Model: JNM GSX / Field strength: 500 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
EMBOSSstructure solution
X-PLORstructure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD
Software ordinal: 1
NMR ensembleConformer selection criteria: AT FIRST, THE DEPOSITORS CARRIED OUT THE DISTANCE GEOMETRY CALCULATION BY STARTING FROM 55 INITIAL STRUCTURES. THIS CALCULATION RESULTED IN 41 SOLUTIONS, WHICH HAD ...Conformer selection criteria: AT FIRST, THE DEPOSITORS CARRIED OUT THE DISTANCE GEOMETRY CALCULATION BY STARTING FROM 55 INITIAL STRUCTURES. THIS CALCULATION RESULTED IN 41 SOLUTIONS, WHICH HAD CORRECT POLYPEPTIDE FOLDS EXCLUDING 14 MIRROR-IMAGE SUBSTRUCTURES. NEXT, THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS WERE PERFORMED BY USING THESE 41 SUBSTRUCTURES. THE DISTANCE AND TORSION ANGLE VIOLATIONS OF THE 41 SOLUTIONS OBTAINED BY THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS WERE SMALLER THAN 0.6 ANGSTROMS AND 27 DEGREES, RESPECTIVELY. THE DEPOSITORS SELECTED 10 SOLUTIONS THAT HAD THE DISTANCE AND TORSION ANGLE VIOLATIONS OF SMALLER THAN 0.5 ANGSTROMS AND 10 DEGREES, RESPECTIVELY.
Conformers calculated total number: 55 / Conformers submitted total number: 1

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