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- PDB-5iaz: The C-terminal domain of rice beta-galactosidase 1 -

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Basic information

Entry
Database: PDB / ID: 5iaz
TitleThe C-terminal domain of rice beta-galactosidase 1
Componentsbeta-galactosidase 1
KeywordsHYDROLASE / glycoside hydrolase / exoglycosidase / beta-sandwich
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Beta-galactosidase, beta-sandwich domain / Beta-sandwich domain in beta galactosidase / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsRimlumduan, T. / Hua, Y.-l. / Tanaka, T. / Ketudat-Cairns, J.R.
Funding support Thailand, 1items
OrganizationGrant numberCountry
the Commission on Higher Education of Thailand Thailand
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Structure of a plant beta-galactosidase C-terminal domain
Authors: Rimlumduan, T. / Hua, Y.-L. / Tanaka, T. / Ketudat Cairns, J.R.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Other / Structure summary
Category: citation / database_2 ...citation / database_2 / entity / pdbx_database_status
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-galactosidase 1


Theoretical massNumber of molelcules
Total (without water)13,0301
Polymers13,0301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8220 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein beta-galactosidase 1 / Putative uncharacterized protein


Mass: 13029.779 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 734-851
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: OsI_10152 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: B8ANX7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-1H NOESY
122isotropic22D 1H-1H NOESY
133isotropic33D 1H-15N NOESY
143isotropic33D HNHA
154isotropic12D 1H-15N HSQC
164isotropic12D 1H-13C HSQC
174isotropic13D HNCO
184isotropic13D CBCA(CO)NH
194isotropic13D HN(CA)CB
1104isotropic13D (H)CCH-TOCSY
1114isotropic13D C(CO)NH
1124isotropic13D HBCBCACOCAHA
1134isotropic13D 1H-13C NOESY
1145isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2Onon-labelled_sample95% H2O/5% D2O
solution20.54 mM OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 100 % [U-2H] D2O, 100% D2Onon-labelled_sample100% D2O
solution30.79 mM [U-100% 15N] OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
solution40.5 mM [U-100% 13C; U-100% 15N] OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O13C_15N_sample95% H2O/5% D2O
solution50.18 mM [U-10% 13C] OsBGal1 Cter, 20 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O10%_13C_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMOsBGal1 Cternatural abundance1
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
95 %H2Onatural abundance1
5 %D2O[U-2H]1
0.54 mMOsBGal1 Cternatural abundance2
20 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
100 %D2O[U-2H]2
0.79 mMOsBGal1 Cter[U-100% 15N]3
20 mMsodium phosphatenatural abundance3
100 mMsodium chloridenatural abundance3
95 %H2Onatural abundance3
5 %D2O[U-2H]3
0.5 mMOsBGal1 Cter[U-100% 13C; U-100% 15N]4
20 mMsodium phosphatenatural abundance4
100 mMsodium chloridenatural abundance4
95 %H2Onatural abundance4
5 %D2O[U-2H]4
0.18 mMOsBGal1 Cter[U-10% 13C]5
20 mMsodium phosphatenatural abundance5
100 mMsodium chloridenatural abundance5
95 %H2Onatural abundance5
5 %D2O[U-2H]5
Sample conditionsIonic strength: 120 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY INOVAVarianUNITY INOVA5001
Bruker AVANCE DRXBrukerAVANCE DRX8002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
X-PLORv3.1Brungerrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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