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- PDB-8sqx: Solution structure of the basal pilin SpaB from Corynebacterium d... -

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Basic information

Entry
Database: PDB / ID: 8sqx
TitleSolution structure of the basal pilin SpaB from Corynebacterium diphtheriae
ComponentsPutative surface anchored protein
KeywordsCELL ADHESION / Pilin / Basal / Minor / Isopeptide
Function / homologyPrealbumin-like fold domain / Prealbumin-like fold domain / carbohydrate metabolic process / Immunoglobulin-like fold / membrane / Putative surface anchored protein
Function and homology information
Biological speciesCorynebacterium diphtheriae NCTC 13129 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSue, C.K. / Mahoney, B.J. / Cheung, N.A. / Clubb, R.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI52217 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007185 United States
CitationJournal: Biopolymers / Year: 2024
Title: The basal and major pilins in the Corynebacterium diphtheriae SpaA pilus adopt similar structures that competitively react with the pilin polymerase.
Authors: Sue, C.K. / Cheung, N.A. / Mahoney, B.J. / McConnell, S.A. / Scully, J.M. / Fu, J.Y. / Chang, C. / Ton-That, H. / Loo, J.A. / Clubb, R.T.
History
DepositionMay 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.year
Revision 1.3May 15, 2024Group: Database references / Category: 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: Putative surface anchored protein


Theoretical massNumber of molelcules
Total (without water)13,6051
Polymers13,6051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative surface anchored protein


Mass: 13605.122 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Gene: DIP2011 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6NF83

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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
122isotropic12D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
1101isotropic13D HNCO
191isotropic13D HBHA(CO)NH
181isotropic13D HNHA
171isotropic13D HNHB
161isotropic23D H(CCO)NH
1132isotropic23D (H)CCH-COSY
1122isotropic23D (H)CCH-TOCSY
1111isotropic13D 1H-15N TOCSY
1161isotropic23D 1H-15N NOESY
1152isotropic23D 1H-13C NOESY aliphatic
1141isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.2 mM [U-13C; U-15N] SpaB, 50 mM sodium phosphate, 100 mM sodium chloride, 0.01 % sodium azide, 93% H2O/7% D2OSpaB_h2o93% H2O/7% D2O
solution21.2 mM [U-13C; U-15N] SpaB, 50 mM sodium phosphate, 100 mM sodium chloride, 0.01 % sodium azide, 100% D2OSpaB_d2o100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMSpaB[U-13C; U-15N]1
50 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
0.01 %sodium azidenatural abundance1
1.2 mMSpaB[U-13C; U-15N]2
50 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
0.01 %sodium azidenatural abundance2
Sample conditionsIonic strength: 100 mM / Label: SpaB_conditions / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD6001
Bruker AVANCE NEOBrukerAVANCE NEO8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH3.6Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH3.6Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
Xipp1.21.7Dan Garrettchemical shift assignment
Xipp1.21.7Dan Garrettpeak picking
UNIOTorsten Herrmannstructure calculation
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYNational Magnetic Resonance Facility at Madison (Wisconsin)data analysis
TALOS-NCornilescu, Delaglio and Baxgeometry optimization
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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