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- PDB-2ltj: Conformational analysis of StrH, the surface-attached exo- beta-D... -

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Basic information

Entry
Database: PDB / ID: 2ltj
TitleConformational analysis of StrH, the surface-attached exo- beta-D-N-acetylglucosaminidase from Streptococcus pneumoniae
ComponentsBeta-N-acetylhexosaminidaseHexosaminidase
KeywordsHYDROLASE / elongated / b-sheet
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / G5 domain / G5 domain / G5 domain profile. / G5 / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide ...Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / G5 domain / G5 domain / G5 domain profile. / G5 / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single Sheet / Glycoside hydrolase superfamily / Mainly Beta
Similarity search - Domain/homology
Beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 21
Model type detailsminimized average
AuthorsPluvinage, B. / Chitayat, S. / Ficko-Blean, E. / Abbott, D. / Kunjachen, J. / Grondin, J. / Spencer, H. / Smith, S. / Boraston, A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Conformational analysis of StrH, the surface-attached exo-beta-D-N-acetylglucosaminidase from Streptococcus pneumoniae.
Authors: Pluvinage, B. / Chitayat, S. / Ficko-Blean, E. / Abbott, D.W. / Kunjachen, J.M. / Grondin, J. / Spencer, H.L. / Smith, S.P. / Boraston, A.B.
History
DepositionMay 28, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
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 / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase


Theoretical massNumber of molelcules
Total (without water)12,2931
Polymers12,2931
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)21 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 12292.636 Da / Num. of mol.: 1 / Fragment: G5 1 domain residues 1050-1140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: strH, SP_0057 / Production host: Escherichia coli (E. coli) / References: UniProt: P49610, beta-N-acetylhexosaminidase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1312D 1H-1H NOESY
1412D 1H-1H TOCSY
1513D C(CO)NH
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] G5, 25 mM TRIS, 25 mM sodium chloride, 0.5 mM DSS, 1 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMG5-1[U-100% 13C; U-100% 15N]1
25 mMTRIS-21
25 mMsodium chloride-31
0.5 mMDSS-41
1 mMDTT-51
Sample conditionsIonic strength: 0.025 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
VnmrJVariancollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THERE WERE NO RESTRAINTS FOR THE HIS-TAG REGION OF THE PROTEIN.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 21

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