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- PDB-6m3a: Staphylococcus aureus Bap-C1 -

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Basic information

Entry
Database: PDB / ID: 6m3a
TitleStaphylococcus aureus Bap-C1
ComponentsBiofilm-associated surface protein
KeywordsUNKNOWN FUNCTION / biofilm associated protein
Function / homology
Function and homology information


cell-abiotic substrate adhesion / single-species submerged biofilm formation / cell-cell adhesion / extracellular region / metal ion binding / membrane
Similarity search - Function
Bacterial Ig domain / Bacterial Ig 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-like fold / Immunoglobulins / Immunoglobulin-like ...Bacterial Ig domain / Bacterial Ig 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-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biofilm-associated surface protein
Similarity search - Component
Biological speciesStaphylococcus aureus VET0329R (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsFang, X. / Ning, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Solution structure of Staphylococcus aureus Bap_C1
Authors: Ning, X. / Fang, X.
History
DepositionMar 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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: Biofilm-associated surface protein


Theoretical massNumber of molelcules
Total (without water)11,1021
Polymers11,1021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7690 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Biofilm-associated surface protein / Bap-C1


Mass: 11101.702 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus VET0329R (bacteria)
Gene: bap
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q79LN3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HBHA(CO)NH
161isotropic13D (H)CCH-TOCSY
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY
191isotropic13D HNCO

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Sample preparation

DetailsType: solution
Contents: 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O
Details: 20mM Sodium phosphate pH7.4 100mM NaCl / Label: 15N_sample, 13C-sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
Sample conditionsDetails: 20mM Sodium phosphate pH7.4 100mM NaCl / Ionic strength: 20 mM / Label: Bap-C1 solution buffer / pH: 7.4 / Pressure: 760 mmHg / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: HCN TCI probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 6
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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