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- PDB-2nd4: A distinct sortase SrtB anchors and processes a streptococcal adh... -

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Basic information

Entry
Database: PDB / ID: 2nd4
TitleA distinct sortase SrtB anchors and processes a streptococcal adhesin AbpA with a novel structural property
ComponentsAmylase-binding protein AbpA
KeywordsHYDROLASE RECEPTOR / Novel Fold
Function / homology: / Amylase-binding protein AbpA / Amylase-binding protein AbpA
Function and homology information
Biological speciesStreptococcus parasanguinis FW213 (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model1
AuthorsLiu, B. / Zhu, F. / Wu, H. / Matthews, S.
CitationJournal: Sci Rep / Year: 2016
Title: A distinct sortase SrtB anchors and processes a streptococcal adhesin AbpA with a novel structural property.
Authors: Liang, X. / Liu, B. / Zhu, F. / Scannapieco, F.A. / Haase, E.M. / Matthews, S. / Wu, H.
History
DepositionMay 5, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amylase-binding protein AbpA


Theoretical massNumber of molelcules
Total (without water)19,1241
Polymers19,1241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Amylase-binding protein AbpA


Mass: 19123.781 Da / Num. of mol.: 1 / Fragment: residues 25-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus parasanguinis FW213 (bacteria)
Gene: abpA, Spaf_0022, UA01_01996 / Production host: Escherichia coli (E. coli) / References: UniProt: I1ZJ30

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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
1313D HN(CA)CB
1413D HNCO
1513D HNCA
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D (H)CCH-TOCSY
1913D HBHA(CO)NH
1101(H)CC(CO)NH-TOCSY

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Sample preparation

DetailsContents: 50 mM sodium chloride, 100 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMsodium chloride-11
100 mMpotassium phosphate-21
Sample conditionspH: 5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificdata analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 1

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