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- PDB-6so0: NMR solution structure of the family 14 carbohydrate binding modu... -

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Basic information

Entry
Database: PDB / ID: 6so0
TitleNMR solution structure of the family 14 carbohydrate binding module (CBM14) from human chitotriosidase
ComponentsChitotriosidase-1
KeywordsSUGAR BINDING PROTEIN / CBM / hevein like fold / chitin binding / chitotriosidase
Function / homology
Function and homology information


endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium / specific granule lumen / tertiary granule lumen / lysosome / immune response / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsMadland, E. / Crasson, O. / Vandevenne, M. / Sorlie, M. / Aachmann, F.L.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway226244 Norway
CitationJournal: Acs Omega / Year: 2019
Title: NMR and Fluorescence Spectroscopies Reveal the Preorganized Binding Site in Family 14 Carbohydrate-Binding Module from Human Chitotriosidase.
Authors: Madland, E. / Crasson, O. / Vandevenne, M. / Sorlie, M. / Aachmann, F.L.
History
DepositionAug 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Chitotriosidase-1


Theoretical massNumber of molelcules
Total (without water)6,2011
Polymers6,2011
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4690 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Chitotriosidase-1 / Chitinase-1


Mass: 6201.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHIT1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13231, chitinase

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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
132isotropic12D 1H-13C HSQC aliphatic
142isotropic13D HNCA
152isotropic13D HNCO
162isotropic13D CBCA(CO)NH
172isotropic13D HN(CA)CB
192isotropic13D HN(CO)CA
182isotropic13D (H)CCH-TOCSY
1142isotropic13D H(CCO)NH
1132isotropic13D 1H-15N NOESY
1122isotropic13D 1H-13C NOESY aliphatic
2113isotropic12D 1H-1H NOESY
2103isotropic12D 1H-1H COSY
2153isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.1 mM [U-98% 15N] CBM14, 50 mM sodium phosphate, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.1 mM [U-98% 13C; U-98% 15N] CBM14, 50 mM sodium phosphate, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution30.1 mM CBM14, 50 mM sodium phosphate, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMCBM14[U-98% 15N]1
50 mMsodium phosphatenatural abundance1
0.1 mMCBM14[U-98% 13C; U-98% 15N]2
50 mMsodium phosphatenatural abundance2
0.1 mMCBM14natural abundance3
50 mMsodium phosphatenatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Details
10.11 Mconditions_15.5 1 atm298.1 K
20.11 Mconditions_25.5 1 atm298.1 KSample was freeze dried and dissolved in D2O

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.5Keller and Wuthrichdata analysis
XEASYBartels et al.data analysis
YASARAKrieger, Darden, Nabuurs, Finkelstein, Vriendrefinement
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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