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- PDB-5x5s: Ligand induced structure of AmyP-SBD -

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Basic information

Entry
Database: PDB / ID: 5x5s
TitleLigand induced structure of AmyP-SBD
ComponentsAmylase
KeywordsHYDROLASE / Starch binding domain / Ligand induced structure / Alpha-amylase
Function / homologyAlpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / catalytic activity / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / carbohydrate metabolic process / Amylase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodSOLUTION NMR / simulated annealing
AuthorsLi, X. / Yu, J. / Sun, H. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese National Natural Science Foundation31470775 China
CitationJournal: To Be Published
Title: Ligand binding induced folding of a novel CBM69 starch binding domain
Authors: Li, X. / Yu, J. / Tu, X. / Sun, H. / Peng, H. / Zhang, X.
History
DepositionFeb 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_ensemble / pdbx_nmr_refine / pdbx_nmr_representative / pdbx_nmr_software
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_ensemble.conformer_selection_criteria / _pdbx_nmr_refine.method / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amylase


Theoretical massNumber of molelcules
Total (without water)17,0241
Polymers17,0241
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10570 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Amylase / / Putative amylase


Mass: 17023.881 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 491-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: Amy-1E / Production host: Escherichia coli (E. coli) / References: UniProt: D9MZ14

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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
121isotropic13D 1H-15N TOCSY
131isotropic13D 1H-15N NOESY
142isotropic22D 1H-15N HSQC
152isotropic23D CBCA(CO)NH
162isotropic23D CBCANH
172isotropic23D HBHA(CO)NH
182isotropic23D HCC(CO)NH
192isotropic23D CC(CO)NH
1102isotropic23D HNCO
1112isotropic23D 1H-15N NOESY
1122isotropic23D HNCA
1132isotropic23D HN(CO)CA
1143isotropic23D (H)CCH-TOCSY
1153isotropic23D (H)CCH-COSY
1163isotropic23D 1H-13C NOESY
1173isotropic22D 1H-13C HSQC
1183isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.4 mM [U-99% 15N] AmyP-SBD, 2 mM NA- beta-cyclodextrin, 90% H2O/10% D2OThe added beta-cyclodextrin was used to incuce AmyP-SBD to fold.15N_sample90% H2O/10% D2O
solution20.4 mM [U-99% 13C; U-99% 15N] AmyP-SBD, 2 mM NA beta-cyclodextrin, 90% H2O/10% D2OThe added beta-cyclodextrin was used to induce AmyP-SBD fold15N/13C_sample90% H2O/10% D2O
solution30.4 mM [U-99% 13C; U-99% 15N] AmyP-SBD, 2 mM NA beta-cyclodextrin, 100% D2OThe added beta-cyclodextrin was used to induce AmyP-SBD fold15N/13C_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMAmyP-SBD[U-99% 15N]1
2 mMbeta-cyclodextrinNA-1
0.4 mMAmyP-SBD[U-99% 13C; U-99% 15N]2
2 mMbeta-cyclodextrinNA2
0.4 mMAmyP-SBD[U-99% 13C; U-99% 15N]3
2 mMbeta-cyclodextrinNA3
Sample conditionsDetails: 20 mM NaH2PO4 containing 100 mM NaCl, pH 6.5, 90% H2O/10% D2O
Ionic strength: 0.12 M / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER, ADAMS, CLORE, GROS, NILGES AND READrefinement
CNSstructure solution
Sparkystructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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