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- PDB-7ofn: NMR solution structure of the SYLF domain of Burkholderia pseudom... -

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Basic information

Entry
Database: PDB / ID: 7ofn
TitleNMR solution structure of the SYLF domain of Burkholderia pseudomallei BPSL1445
ComponentsLipoprotein
KeywordsLIPID BINDING PROTEIN / Burkholderia pseudomallei Lipoprotein SYLF domain beta berrel
Function / homologyYsc84 actin-binding domain / Las17-binding protein actin regulator / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsQuilici, G. / Berardi, A. / Musco, G.
Funding support Italy, 2items
OrganizationGrant numberCountry
Fondazione CARIPLO2009-3577 Italy
Italian Association for Cancer ResearchIG-214400 Italy
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Solution Structure of the BPSL1445 Protein of Burkholderia pseudomallei Reveals the SYLF Domain Three-Dimensional Fold.
Authors: Quilici, G. / Berardi, A. / Fabris, C. / Ghitti, M. / Punta, M. / Gourlay, L.J. / Bolognesi, M. / Musco, G.
History
DepositionMay 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 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: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)16,5371
Polymers16,5371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Confirmed by NMR relaxation
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lipoprotein


Mass: 16536.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GS do not belong to the real sequence, they derive from the vector region, to match pdb sequence numbering to BPSL1445 sequence add 32
Source: (gene. exp.) Burkholderia pseudomallei (bacteria)
Gene: BOC42_05350, CXQ84_09430, DF122_22840, ERS013345_04496
Plasmid: pGEX-4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069B8F8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
122isotropic12D 1H-1H NOESY
133isotropic13D 1H-15N NOESY
144isotropic13D 1H-13C NOESY
155isotropic13D C(CO)NH
175isotropic13D H(CCO)NH
165isotropic13D HNCA
185isotropic13D HNCO
194isotropic13D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.3 mM BPSL1445, 150 mM sodium chloride, 20 mM NaH2PO4, 20 mM Na2HPO4, 2 mM DTT, 90% H2O/10% D2Ounlabel_water90% H2O/10% D2O
solution20.3 mM BPSL1445, 150 mM sodium chloride, 20 mM NaH2PO4, 20 mM Na2HPO4, 2 mM DTT, 100% D2Ounlabel_D2O100% D2O
solution30.3 mM BPSL1445, 150 mM sodium chloride, 20 mM NaH2PO4, 20 mM Na2HPO4, 2 mM DTT, 90% H2O/10% D2O15N_H2O90% H2O/10% D2O
solution40.3 mM BPSL1445, 150 mM sodium chloride, 20 mM NaH2PO4, 20 mM Na2HPO4, 2 mM DTT, 100% D2O15N_13C_D2O100% D2O
solution50.3 mM BPSL1445, 150 mM sodium chloride, 20 mM NaH2PO4, 20 mM Na2HPO4, 2 mM DTT, 90% H2O/10% D2O15N_13C_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMBPSL1445natural abundance1
150 mMsodium chloridenatural abundance1
20 mMNaH2PO4natural abundance1
20 mMNa2HPO4natural abundance1
2 mMDTTnatural abundance1
0.3 mMBPSL1445natural abundance2
150 mMsodium chloridenatural abundance2
20 mMNaH2PO4natural abundance2
20 mMNa2HPO4natural abundance2
2 mMDTTnatural abundance2
0.3 mMBPSL1445natural abundance3
150 mMsodium chloridenatural abundance3
20 mMNaH2PO4natural abundance3
20 mMNa2HPO4natural abundance3
2 mMDTTnatural abundance3
0.3 mMBPSL1445natural abundance4
150 mMsodium chloridenatural abundance4
20 mMNaH2PO4natural abundance4
20 mMNa2HPO4natural abundance4
2 mMDTTnatural abundance4
0.3 mMBPSL1445natural abundance5
150 mMsodium chloridenatural abundance5
20 mMNaH2PO4natural abundance5
20 mMNa2HPO4natural abundance5
2 mMDTTnatural abundance5
Sample conditionsIonic strength: 150 mM / Label: standard_conditions / pH: 6.3 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospinrefinement
ARIA3.2Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr Analysis2.4CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 10

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