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- PDB-2rva: Solution structure of chitosan-binding module 2 derived from chit... -

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Basic information

Entry
Database: PDB / ID: 2rva
TitleSolution structure of chitosan-binding module 2 derived from chitosanase/glucanase from Paenibacillus sp. IK-5
ComponentsGlucanase
KeywordsHYDROLASE / carbohydrate-binding module / CBM / chitosanase
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / NedA-like, galactose-binding domain / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Six-hairpin glycosidase-like superfamily ...Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / NedA-like, galactose-binding domain / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose-binding domain-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus fukuinensis (bacteria)
MethodSOLUTION NMR / na
Model detailslowest energy, model1
AuthorsShinya, S. / Nishimura, S. / Fukamizo, T.
CitationJournal: Biochem.J. / Year: 2016
Title: Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase.
Authors: Shinya, S. / Nishimura, S. / Kitaoku, Y. / Numata, T. / Kimoto, H. / Kusaoke, H. / Ohnuma, T. / Fukamizo, T.
History
DepositionMay 13, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucanase


Theoretical massNumber of molelcules
Total (without water)14,9101
Polymers14,9101
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)10 / 28000target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Glucanase / chitosanase


Mass: 14910.056 Da / Num. of mol.: 1 / Fragment: chitosan-binding module 2, UNP residues 666-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus fukuinensis (bacteria)
Description: Paenibacillus fukuinensis has been renamed to Paenibacillus sp. IK-5.
Production host: Escherichia coli (E. coli)
References: UniProt: Q93IE7, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D 1H-15N NOESY
1713D CBCA(CO)NH
1822D 1H-13C HSQC
1923D (H)CCH-TOCSY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM TRIS-1, 0.4 mM [U-95% 13C; U-95% 15N] DD2-2, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-95% 13C; U-95% 15N] DD2-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMTRIS-11
0.4 mMDD2-2[U-95% 13C; U-95% 15N]1
0.4 mMDD2-3[U-95% 13C; U-95% 15N]2
Sample conditionspH: 7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: na / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 28000 / Conformers submitted total number: 10 / Representative conformer: 1

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