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- PDB-2m6u: NMR Structure of CbpAN from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 2m6u
TitleNMR Structure of CbpAN from Streptococcus pneumoniae
ComponentsCholine binding protein A
KeywordsCHOLINE-BINDING PROTEIN / three-helix bundle / CHOLINE BINDING PROTEIN
Function / homologyReceptor-associated Protein - #20 / Receptor-associated Protein / Up-down Bundle / Mainly Alpha / :
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsclosest to the average, model10
AuthorsLiu, A. / Yan, H. / Achila, D. / Martinez-Hackert, E. / Li, Y. / Banerjee, R.
CitationJournal: Biochem.J. / Year: 2015
Title: Structural determinants of host specificity of complement Factor H recruitment by Streptococcus pneumoniae.
Authors: Achila, D. / Liu, A. / Banerjee, R. / Li, Y. / Martinez-Hackert, E. / Zhang, J.R. / Yan, H.
History
DepositionApr 10, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_keywords / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.4May 15, 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: Choline binding protein A


Theoretical massNumber of molelcules
Total (without water)9,8491
Polymers9,8491
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 / 50target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Choline binding protein A / CbpA


Mass: 9849.235 Da / Num. of mol.: 1 / Fragment: UNP residues 67-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SPAR136_2333 / Plasmid: pET17bHR / Production host: Escherichia coli (E. coli) / References: UniProt: G6W2B2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: after energy minimization with AMBER
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCO
1713D HN(CA)CO
1813D 1H-15N NOESY
1922D 1H-13C HSQC
11023D (H)CCH-TOCSY
11123D 1H-13C NOESY aliphatic
11223D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
150 uM DSS, 100 uM sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
250 uM DSS, 100 uM sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 uMDSS-11
100 uMsodium azide-21
50 mMsodium phosphate-31
50 mMsodium chloride-41
50 uMDSS-52
100 uMsodium azide-62
50 mMsodium phosphate-72
50 mMsodium chloride-82
Sample conditionsIonic strength: 100 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 75 / Protein psi angle constraints total count: 75
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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