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- PDB-2djm: Solution structure of N-terminal starch-binding domain of glucoam... -

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Basic information

Entry
Database: PDB / ID: 2djm
TitleSolution structure of N-terminal starch-binding domain of glucoamylase from Rhizopus oryzae
Componentsglucoamylase A
KeywordsSUGAR BINDING PROTEIN / beta sandwich / anti-parallel / strach binding / carbohydrate binding
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / polysaccharide catabolic process
Similarity search - Function
Carbohydrate binding type-21 domain / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Glucoamylase / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Six-hairpin glycosidase-like superfamily ...Carbohydrate binding type-21 domain / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Glucoamylase / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRhizopus oryzae (fungus)
MethodSOLUTION NMR / torsion angle dynamics, distance geometry, simulated annealing, water refine
AuthorsLiu, Y.N. / Lai, Y.T. / Lyu, P.C.
CitationJournal: Biochem.J. / Year: 2007
Title: Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase
Authors: Liu, Y.N. / Lai, Y.T. / Chou, W.I. / Chang, M.D.T. / Lyu, P.C.
History
DepositionApr 4, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glucoamylase A


Theoretical massNumber of molelcules
Total (without water)11,6631
Polymers11,6631
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)15 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein glucoamylase A / Family 21 carbohydrate-binding module


Mass: 11662.581 Da / Num. of mol.: 1 / Fragment: Starch-binding domain, resdiues 1-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizopus oryzae (fungus) / Gene: amyA / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 82491809, UniProt: P07683*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
1423D N15 HSQC TOCSY
1523D N15 HSQC NOESY
163CBCA(CO)NH; HN(CA)CB
NMR detailsText: The structure was determined using both 2D homonuclear and triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM SBD (unlabel); 10mM sodium acttate pH4.5; 10% D2O, 90% H2O10% D2O; 90% H2O
2N15 label 1mM SBD; 10mM sodium acttate pH4.5; 10% D2O, 90% H2O10% D2O; 90% H2O
3N15,C13 double label 1mM SBD; 10mM sodium acttate pH4.5; 10% D2O, 90% H2O10% D2O; 90% H2O
Sample conditionsIonic strength: 10mM sodium acetate / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
TopSpin1.3Brukerprocessing
Sparky3.111Goddard, T.D., Kneller, D.G.data analysis
CNS1.1structure solution
ARIA2Nilges, M., O'Donoghue, S.I.refinement
RefinementMethod: torsion angle dynamics, distance geometry, simulated annealing, water refine
Software ordinal: 1
Details: the structures are based on a total of 2414 restraints, 2238 are NOE-derived distance constraints, 102 dihedral angle restraints,74 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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