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- PDB-1prb: STRUCTURE OF AN ALBUMIN-BINDING DOMAIN, NMR, MINIMIZED AVERAGE ST... -

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Basic information

Entry
Database: PDB / ID: 1prb
TitleSTRUCTURE OF AN ALBUMIN-BINDING DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsPROTEIN PAB
KeywordsALBUMIN-BINDING PROTEIN / BACTERIAL SURFACE PROTEINS / EVOLUTION / MODULE SHUFFLING
Function / homology
Function and homology information


Albumin-binding domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Helicase, Ruva Protein; domain 3 ...Albumin-binding domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peptostreptococcal albumin-binding protein
Similarity search - Component
Biological speciesFinegoldia magna ATCC 29328 (bacteria)
MethodSOLUTION NMR / DETAILS OF THE STRUCTURE DETERMINATION, ALL STRUCTURAL STATISTICS ARE GIVEN IN THE PAPER CITED ON THE JRNL RECORDS ABOVE. THE STRUCTURES ARE BASED ON 649 INTERPROTON DISTANCE CONSTRAINTS, 26 DIHEDRAL CONSTRAINTS. NO HYDROGEN BOND CONSTRAINTS WERE USED.
AuthorsJohansson, M.U. / De Chateau, M. / Wikstrom, M. / Forsen, S. / Drakenberg, T. / Bjorck, L.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Solution structure of the albumin-binding GA module: a versatile bacterial protein domain.
Authors: Johansson, M.U. / de Chateau, M. / Wikstrom, M. / Forsen, S. / Drakenberg, T. / Bjorck, L.
#1: Journal: FEBS Lett. / Year: 1995
Title: The Ga Module, a Mobile Albumin-Binding Bacterial Domain, Adopts a Three-Helix-Bundle Structure
Authors: Johansson, M.U. / De Chateau, M. / Bjorck, L. / Forsen, S. / Drakenberg, T. / Wikstrom, M.
History
DepositionJan 15, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_representative / pdbx_nmr_software / pdbx_nmr_spectrometer / 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.authors / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
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: PROTEIN PAB


Theoretical massNumber of molelcules
Total (without water)5,9401
Polymers5,9401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200THE AVERAGE STRUCTURE PRESENTED IN THIS ENTRY IS BASED ON 20 STRUCTURES SELECTED ON THE BASIS OF CONSTRAINT VIOLATIONS
RepresentativeModel #1closest to the average

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Components

#1: Protein PROTEIN PAB / GA MODULE


Mass: 5939.786 Da / Num. of mol.: 1 / Fragment: ALBUMIN-BINDING DOMAIN, RESIDUES 213 - 265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna ATCC 29328 (bacteria) / Species: Finegoldia magna / Strain: ALB8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51911

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121R-COSY
131TOCSY
1412Q
151NOESY

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Sample preparation

Sample conditionspH: 6 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA5001
Varian UNITYVarianUNITY5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure calculation
RefinementMethod: DETAILS OF THE STRUCTURE DETERMINATION, ALL STRUCTURAL STATISTICS ARE GIVEN IN THE PAPER CITED ON THE JRNL RECORDS ABOVE. THE STRUCTURES ARE BASED ON 649 INTERPROTON DISTANCE CONSTRAINTS, 26 ...Method: DETAILS OF THE STRUCTURE DETERMINATION, ALL STRUCTURAL STATISTICS ARE GIVEN IN THE PAPER CITED ON THE JRNL RECORDS ABOVE. THE STRUCTURES ARE BASED ON 649 INTERPROTON DISTANCE CONSTRAINTS, 26 DIHEDRAL CONSTRAINTS. NO HYDROGEN BOND CONSTRAINTS WERE USED.
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: THE AVERAGE STRUCTURE PRESENTED IN THIS ENTRY IS BASED ON 20 STRUCTURES SELECTED ON THE BASIS OF CONSTRAINT VIOLATIONS
Conformers calculated total number: 200 / Conformers submitted total number: 1

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