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- PDB-2mxx: Structure of Amylase binding Protein A of Streptococcous gordonii... -

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Basic information

Entry
Database: PDB / ID: 2mxx
TitleStructure of Amylase binding Protein A of Streptococcous gordonii: a potential receptor for human salivary amylase enzyme
ComponentsAmylase-binding protein AbpA
KeywordsHYDROLASE RECEPTOR
Function / homology: / Amylase-binding protein AbpA / nucleic acid binding / Amylase-binding protein AbpA
Function and homology information
Biological speciesStreptococcus gordonii str. Challis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, energy minimization
Model detailsclosest to the average, model5
AuthorsSethi, A. / Mohanty, B. / Ramasubbu, N. / Gooley, P.R.
CitationJournal: Protein Sci. / Year: 2015
Title: Structure of amylase-binding protein A of Streptococcus gordonii: A potential receptor for human salivary alpha-amylase enzyme.
Authors: Sethi, A. / Mohanty, B. / Ramasubbu, N. / Gooley, P.R.
History
DepositionJan 18, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: 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 / 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

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Assembly

Deposited unit
A: Amylase-binding protein AbpA


Theoretical massNumber of molelcules
Total (without water)19,1711
Polymers19,1711
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)20 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Amylase-binding protein AbpA


Mass: 19170.777 Da / Num. of mol.: 1 / Fragment: residues 24-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii str. Challis (bacteria)
Strain: Challis / Gene: abpA, SGO_2105 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A8AZZ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D HN(CA)CO
1513D CC(CO)NH
1613D (H)CC(CO)NH
1713D 15N resolved [1H,1H]-NOESY
1813D 13Cali resolved [1H,1H]-NOESY
1913D 13Caro resolved [1H,1H]-NOESY
11012D 15N{1H}-NOE

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Sample preparation

DetailsContents: 325 uM U-98% 13C, U-98% 15N AbpA, 93% H2O/7% D2O / Solvent system: 93% H2O/7% D2O
SampleConc.: 325 uM / Component: AbpA-1 / Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionsIonic strength: 100 / pH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospindata collection
TopSpin3.2Bruker Biospinprocessing
CARA1.5.3Keller and Wuthrichchemical shift assignment
CARA1.5.3Keller and Wuthrichpeak picking
UNIO2.0.1Herrmann and Wuthrichpeak picking
UNIO2.0.1Herrmann and Wuthrichnoe assignment
UNIO2.0.1Herrmann and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
OPALp1.2Koradi,Billeter and Guntertrefinement
RefinementMethod: torsion angle dynamics, energy minimization / Software ordinal: 1
NMR constraintsNOE constraints total: 1774 / NOE intraresidue total count: 402 / NOE long range total count: 194 / NOE medium range total count: 536 / NOE sequential total count: 642
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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