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- PDB-5wah: SOLUTION NMR STRUCTURE OF SIGLEC-5 BINDING DOMAIN FROM STREPTOCOC... -

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Basic information

Entry
Database: PDB / ID: 5wah
TitleSOLUTION NMR STRUCTURE OF SIGLEC-5 BINDING DOMAIN FROM STREPTOCOCCAL BETA PROTEIN
ComponentsIgA FC receptor
KeywordsPROTEIN BINDING / IGA-FC RECEPTOR / THREE-HELIX BUNDLE / BETA ANTIGEN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Surface antigen, GAG-binding domain / Surface antigen, GAG-binding domain superfamily / GAG-binding domain on surface antigen / RICH domain / RICH domain superfamily / RICH domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...Surface antigen, GAG-binding domain / Surface antigen, GAG-binding domain superfamily / GAG-binding domain on surface antigen / RICH domain / RICH domain superfamily / RICH domain / 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 / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesStreptococcus agalactiae (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsELETSKY, A. / CHEN, C. / FONG, J.J. / NIZET, V. / VARKI, A. / PRESTEGARD, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1021RR549545 United States
CitationJournal: To Be Published
Title: SOLUTION NMR STRUCTURE OF SIGLEC-5 BINDING DOMAIN FROM STREPTOCOCCAL BETA PROTEIN
Authors: ELETSKY, A. / CHEN, C. / FONG, J.J. / NIZET, V. / VARKI, A. / PRESTEGARD, J.H.
History
DepositionJun 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IgA FC receptor


Theoretical massNumber of molelcules
Total (without water)11,5141
Polymers11,5141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Monomeric state confirmed by measuring average 15N T1 and T2 relaxation times in 1D NMR relaxation experiments
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein IgA FC receptor / Beta antigen / B antigen


Mass: 11513.662 Da / Num. of mol.: 1 / Fragment: UNP residues 92-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: bag / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27951

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
121isotropic32D 1H-13C CT-HSQC aliphatic
131isotropic32D 1H-13C CT-HSQC aromatic
141isotropic13D HNCO
151isotropic23D CBCA(CO)NH
171isotropic13D HN(CA)CB
1121isotropic13D (H)CA(CO)NH
1111isotropic23D HBHA(CO)NH
1101isotropic43D (H)CCH-COSY aliphatic
191isotropic43D (H)CCH-COSY aromatic
181isotropic33D (H)CCH-TOCSY aliphatic
161isotropic43D 1H-15N NOESY
1131isotropic43D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.45 mM [U-13C; U-15N] IgA-Fc Receptor, 20 mM sodium phosphate, 4 uM DSS, 0.01 % sodium azide, 100 mM sodium chloride, 90% H2O/10% D2O
Details: 90 ul in a 3 mm shigemi tube / Label: NC / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.45 mMIgA-Fc Receptor[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
4 uMDSSnatural abundance1
0.01 %sodium azidenatural abundance1
100 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 130 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Agilent DD2AgilentDD260013MM CRYOGENIC PROBE
Varian VNMRSVarianVNMRS60025MM CRYOGENIC PROBE
Agilent DD2AgilentDD290035MM CRYOGENIC PROBE
Agilent DD2AgilentDD280045MM CRYOGENIC PROBE

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CARA1.9.1.7Keller and Wuthrichpeak picking
VnmrJ4.2AVariancollection
NMRPipe8.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running CYANA and AS-DP in parallel using NOE-based distance constraints and PHI, PSI and CHI1 dihedral angle constraints from TALOS-N. Consensus ...Details: Structure determination was performed by running CYANA and AS-DP in parallel using NOE-based distance constraints and PHI, PSI and CHI1 dihedral angle constraints from TALOS-N. Consensus peak assignments were selected and used in iterative refinement with CYANA. 20 conformers with the lowest target function out of 100 were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field and upper limit distance constraints relaxed by 5%
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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