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- PDB-2fs1: solution structure of PSD-1 -

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Basic information

Entry
Database: PDB / ID: 2fs1
Titlesolution structure of PSD-1
ComponentsPSD-1
KeywordsPROTEIN BINDING / solution structure / PSD-1
Function / homology
Function and homology information


IgG binding / immunoglobulin binding
Similarity search - Function
Albumin-binding domain / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Repeat of unknown function DUF5633 / Protein L b1 domain / Family of unknown function (DUF5633) / GA-like domain ...Albumin-binding domain / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Repeat of unknown function DUF5633 / Protein L b1 domain / 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
Biological speciesFinegoldia magna ATCC 29328 (bacteria)
Streptococcus dysgalactiae (bacteria)
Streptococcus equi (bacteria)
Streptococcus canis (bacteria)
Streptococcus sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHe, Y. / Rozak, D.A. / Sari, N. / Chen, Y. / Bryan, P. / Orban, J.
CitationJournal: Biochemistry / Year: 2006
Title: Structure, dynamics, and stability variation in bacterial albumin binding modules: implications for species specificity.
Authors: He, Y. / Rozak, D.A. / Sari, N. / Chen, Y. / Bryan, P. / Orban, J.
History
DepositionJan 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 999SEQUENCE The protein was obtained by recombining seven artificial constructs that cumulatively ...SEQUENCE The protein was obtained by recombining seven artificial constructs that cumulatively represented much of the genetic diversity found in 16 native albumin binding domains from six proteins and bacterial species namely Peptostreptococcus magnus [L3316-GA1], Streptococcus dysgalactiae [MAG-GA1], Streptococcus equi [ZAG-GA], Streptococcus canis [DG12-GA2], (Rozak, Alexander, et al. Biochemistry 2006, in press). The characters enclosed in square brackets refer to the particular albumin binding domain found in the bacteria. There is no amino acid sequence database reference available for the recombinant protein.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PSD-1


Theoretical massNumber of molelcules
Total (without water)6,1451
Polymers6,1451
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PSD-1


Mass: 6145.015 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna ATCC 29328, Streptococcus dysgalactiae, Streptococcus equi, Streptococcus canis, Streptococcus sp.
Genus: Finegoldia, Streptococcus, Streptococcus, Streptococcus, Streptococcus
Species: Finegoldia magna, , , , / Strain: ATCC 29328, , , , / Plasmid: pG58 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-10 / References: UniProt: Q51918

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1313D HN(CA)CB
1413D HNCO
1513D CBCA(CO)NH
1613DHBHA(CBCACO)NH
1713D(H)C(CO)NH-TOCSY
1813DCCONH 2D-CBHD
1912DCBHE
NMR detailsText: The structure was calculated using 1063 restraints. Model 21 is an average of the 20 conformers calculated from experimental restraints.

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Sample preparation

DetailsContents: 0.2~0.4 mM PSD-1, 50 mM sodium phosphate buffer, pH 7.0, 0.1 mM EDTA, 10% D2O, 90% H2O
Solvent system: 10% D2O, 90% H2O
Sample conditionsIonic strength: 50 mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5collection
NMRPipeDelaglio et al.processing
Sparky3Goddard et al.data analysis
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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