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- PDB-2l4o: Solution structure of the Streptococcus pneumoniae RrgB pilus bac... -

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Basic information

Entry
Database: PDB / ID: 2l4o
TitleSolution structure of the Streptococcus pneumoniae RrgB pilus backbone D1 domain
ComponentsCell wall surface anchor family protein
KeywordsCELL ADHESION / RrgB / Streptococcus pneumoniae / pilus
Function / homology
Function and homology information


membrane => GO:0016020 / membrane
Similarity search - Function
Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Immunoglobulins / Immunoglobulin-like fold ...Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell wall surface anchor family protein / Cell wall surface anchor family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsCING analysis, model 20
AuthorsGentile, M.A. / Melchiorre, S. / Emolo, C. / Moschioni, M. / Gianfaldoni, C. / Pancotto, L. / Ferlenghi, I. / Scarselli, M. / Pansegrau, W. / Veggi, D. ...Gentile, M.A. / Melchiorre, S. / Emolo, C. / Moschioni, M. / Gianfaldoni, C. / Pancotto, L. / Ferlenghi, I. / Scarselli, M. / Pansegrau, W. / Veggi, D. / Merola, M. / Cantini, F. / Ruggiero, P. / Banci, L. / Masignani, V.
CitationJournal: To be Published
Title: Solution structure of the Streptococcus pneumoniae RrgB pilus backbone D1 domain: in vivo protection and implications for the molecular mechanisms of pilus polymerization
Authors: Gentile, M.A. / Melchiorre, S. / Emolo, C. / Moschioni, M. / Gianfaldoni, C. / Pancotto, L. / Ferlenghi, I. / Scarselli, M. / Pansegrau, W. / Veggi, D. / Merola, M. / Cantini, F. / Ruggiero, ...Authors: Gentile, M.A. / Melchiorre, S. / Emolo, C. / Moschioni, M. / Gianfaldoni, C. / Pancotto, L. / Ferlenghi, I. / Scarselli, M. / Pansegrau, W. / Veggi, D. / Merola, M. / Cantini, F. / Ruggiero, P. / Banci, L. / Masignani, V.
History
DepositionOct 11, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)19,3741
Polymers19,3741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400target function
RepresentativeModel #1cing analysis

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Components

#1: Protein Cell wall surface anchor family protein


Mass: 19373.766 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 23-191) / Mutation: BACKBONE SUBUNIT PILI RESIDUES 20-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: rrgB, SP_0463 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q97SC2, UniProt: A0A0H2UNM7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H NOESY
1222D 1H-1H TOCSY
1312D 1H-15N HSQC
1432D 1H-13C HSQC
1533D HN(COCA)CB
1633D HN(CA)CB
1733D HNCO
1833D HN(CO)CA
1933D HBHA(CO)NH
11033D HNCA
11133D HN(CA)CO
11233D (H)CCH-TOCSY
11313D 1H-15N NOESY
11433D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-95% 15N] PROTEIN-1, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM PROTEIN-2, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-95% 13C; U-95% 15N] PROTEIN-3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDOMAIN OF A CELL WALL SURFACE ANCHOR FAMILY PROTEIN-1[U-95% 15N]1
0.9 mMDOMAIN OF A CELL WALL SURFACE ANCHOR FAMILY PROTEIN-22
0.4 mMDOMAIN OF A CELL WALL SURFACE ANCHOR FAMILY PROTEIN-3[U-95% 13C; U-95% 15N]3
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollmrefinement
TopSpin2Bruker Biospinprocessing
CARA2Keller and Wuthrichdata analysis
XEASYBartels et al.data analysis
CINGGeerten W. Vuister , Jurgen F. Doreleijers and Alan Wilter Sousa da Silvastructure validation
MOLMOLKoradi, Billeter and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxcollection
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structures were based on a total of 3131 distance constraints and 234 dihedral angle restraints, 400 random conformers were annealed in 8000 steps
NMR representativeSelection criteria: cing analysis
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20 / Representative conformer: 20
NMR ensemble rmsDistance rms dev: 0.4 Å / Distance rms dev error: 0.15 Å

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