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- PDB-7a2d: Structure-function analyses of dual-BON domain protein DolP ident... -

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Basic information

Entry
Database: PDB / ID: 7a2d
TitleStructure-function analyses of dual-BON domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation to the cell division site
ComponentsUncharacterized protein YraP
KeywordsPROTEIN BINDING / OUTER MEMBRANE BIOGENESIS / GRAM NEGATIVE / LIPOPROTEIN / YRAP / LIPID BIOGENESIS
Function / homology
Function and homology information


response to osmotic stress / cell division site / cell outer membrane / outer membrane-bounded periplasmic space
Similarity search - Function
Transport-associated and nodulation domain, bacteria / bacterial OsmY and nodulation domain / BON domain profile. / BON domain / BON domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Uncharacterized protein YraP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsBryant, J.A. / Morris, F.C. / Knowles, T.J. / Maderbocus, R. / Heinz, E. / Boelter, G. / Alodaini, D. / Colyer, A. / Wotherspoon, P.J. / Staunton, K.A. ...Bryant, J.A. / Morris, F.C. / Knowles, T.J. / Maderbocus, R. / Heinz, E. / Boelter, G. / Alodaini, D. / Colyer, A. / Wotherspoon, P.J. / Staunton, K.A. / Jeeves, M. / Browning, D.F. / Sevastsyanovich, Y.R. / Wells, T.J. / Rossiter, A.E. / Bavro, V.N. / Sridhar, P. / Ward, D.G. / Chong, Z.S. / Goodall, E.C.A. / Icke, C. / Teo, A. / Chng, S.S. / Roper, D.I. / Lithgow, T. / Cunningham, A.F. / Banzhaf, M. / Overduin, M. / Henderson, I.R.
Funding support United Kingdom, Canada, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M00810X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L00335X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P009840/1 United Kingdom
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04994 Canada
CitationJournal: Elife / Year: 2020
Title: Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation.
Authors: Bryant, J.A. / Morris, F.C. / Knowles, T.J. / Maderbocus, R. / Heinz, E. / Boelter, G. / Alodaini, D. / Colyer, A. / Wotherspoon, P.J. / Staunton, K.A. / Jeeves, M. / Browning, D.F. / ...Authors: Bryant, J.A. / Morris, F.C. / Knowles, T.J. / Maderbocus, R. / Heinz, E. / Boelter, G. / Alodaini, D. / Colyer, A. / Wotherspoon, P.J. / Staunton, K.A. / Jeeves, M. / Browning, D.F. / Sevastsyanovich, Y.R. / Wells, T.J. / Rossiter, A.E. / Bavro, V.N. / Sridhar, P. / Ward, D.G. / Chong, Z.S. / Goodall, E.C. / Icke, C. / Teo, A.C. / Chng, S.S. / Roper, D.I. / Lithgow, T. / Cunningham, A.F. / Banzhaf, M. / Overduin, M. / Henderson, I.R.
History
DepositionAug 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / entity ...audit_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Jan 27, 2021Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.3Feb 10, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YraP


Theoretical massNumber of molelcules
Total (without water)19,3251
Polymers19,3251
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12020 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein YraP / DolP


Mass: 19324.738 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 201-91 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yraP, b3150, JW3119, WCM_00535 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P64596

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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
1141isotropic13D (H)CCH-TOCSY
121isotropic13D HN(CO)CA
131isotropic13D HNCA
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
161isotropic13D HNCO
171isotropic13D HN(CA)CO
181isotropic13D (H)CCH-TOCSY
1101isotropic13D 1H-13C NOESY-HSQC ALIPHATIC
1111isotropic13D 1H-13C NOESY-HSQC AROMATIC
1121isotropic13D 1H-15N NOESY-HSQC
1131isotropic1H(C)CONH
NMR detailsText: THE STRUCTURE WAS CALCULATED USING TRADITIONAL NOE AND DEHEDRAL ANGLE RESTRAINTS

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Sample preparation

DetailsType: solution
Contents: 1.5 mM [U-13C; U-15N] DolP, 50 mM NA sodium phosphate, 0.02 % w/v NA NaN3, 50 mM NA sodium chloride, 90% H2O/10% D2O
Details: 1.5 mM 13C-15N labelled DolP in 50 mM sodium phosphate (pH 6), 50 mM NaCl and 0.02% NaN3 in 90% H2O/10% D2O.
Label: 13C-15N-sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMDolP[U-13C; U-15N]1
50 mMsodium phosphateNA1
0.02 % w/vNaN3NA1
50 mMsodium chlorideNA1
Sample conditionsIonic strength: 0.05 M / Label: conditions_1 / pH: 6 / PH err: 0.05 / Pressure: AMBIENT bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3LINGErefinement
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonrefinement
CYANA2.1LASKOWSKI AND MACARTHUR (PROCHECKNMR)refinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
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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