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- PDB-5j8t: NMR structure of Excalibur domain of CbpL -

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Basic information

Entry
Database: PDB / ID: 5j8t
TitleNMR structure of Excalibur domain of CbpL
ComponentsCholine binding protein
KeywordsHYDROLASE / Excalibur / Choline-binding Protein L / Pneumococcal Adhesion
Function / homology:
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsPantoja-Uceda, D. / Trevino, M.A. / Bruix, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessCTQ2014-52633 Spain
CitationJournal: To Be Published
Title: Molecular Choline-bindind Protein L Involved in Pneumococcal Adhesion and Virulence through Exposed Excalibur domanin
Authors: Gutierrez-Fernandez, J. / Alcorlo, M. / Galan-Bartual, S. / Pantoja-Uceda, D. / Trevino, M.A. / Bruix, M. / Hammerschmidt, S. / Hermoso, J.A.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.2Oct 23, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: pdbx_nmr_exptl_sample_conditions / pdbx_nmr_spectrometer ...pdbx_nmr_exptl_sample_conditions / pdbx_nmr_spectrometer / struct_site / struct_site_gen
Item: _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_exptl_sample_conditions.temperature_units / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1862
Polymers5,1451
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area80 Å2
ΔGint-13 kcal/mol
Surface area3860 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein/peptide Choline binding protein


Mass: 5145.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the first three residues GAS correspond to the tag used in the production . the first residue of the protein is the first E in the sequence with the number 24
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: lytB_2, ERS020147_00413 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0U0AG78, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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
132isotropic12D 1H-1H TOCSY
142isotropic12D 1H-1H NOESY
151isotropic13D HNCO
161isotropic13D HNCOi
171isotropic13D HNCA
181isotropic13D HNCAi
191isotropic13D HN(CA)CB
1101isotropic13D CBCA(CO)NH
1111isotropic13D H(CCCO)NH
1121isotropic13D (H)CC(CO)NH
1131isotropic13D (H)CCH-TOCSY
1141isotropic13D (H)CCH-TOCSY
1151isotropic13D H(NCOCA)NH
1161isotropic13D (H)N(COCA)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 13C; U-99% 15N] Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution20.5 mM Excalibur domain of CbpL, 3 mM CaCl2, 1 % DSS, 90% H2O/10% D2O1H_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMExcalibur domain of CbpL[U-99% 13C; U-99% 15N]1
3 mMCaCl2natural abundance1
1 %DSSnatural abundance1
0.5 mMExcalibur domain of CbpLnatural abundance2
3 mMCaCl2natural abundance2
1 %DSSnatural abundance2
Sample conditionsIonic strength: unknown Not defined / Label: conditions_1 / pH: 5.5 Not defined / Pressure: unknown atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz / Details: equiped with cryoprobe TCI

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
NMRView5.0.20Johnson, One Moon Scientificdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Amber9Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 8
Details: the 20 conformers with the lowest targer funciotn values fo CYANA calculation were selected for further refinement and minimized with amber 9.0 using Gibbs-Boltzman continuum solvation model
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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