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- PDB-2jnk: Solution structure of a dockerin-containing modular pair from a f... -

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Basic information

Entry
Database: PDB / ID: 2jnk
TitleSolution structure of a dockerin-containing modular pair from a family 84 glycoside hydrolase
ComponentsHyalurononglucosaminidase
KeywordsHYDROLASE / calcium-binding
Function / homology
Function and homology information


hyaluronoglucosaminidase / hyalurononglucosaminidase activity / glycoprotein metabolic process / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / toxin activity / extracellular region
Similarity search - Function
AF1782-like / FIVAR domain / : / Hyaluronidase post-catalytic domain-like / Type 1 dockerin domain / Dockerin domain / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Beta-hexosaminidase, bacterial type, N-terminal ...AF1782-like / FIVAR domain / : / Hyaluronidase post-catalytic domain-like / Type 1 dockerin domain / Dockerin domain / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / Glycoside hydrolase superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hyaluronoglucosaminidase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsChitayat, S. / Adams, J.J. / Bayer, E.A. / Smith, S.P.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The solution structure of the C-terminal modular pair from Clostridium perfringens mu-toxin reveals a noncellulosomal dockerin module
Authors: Chitayat, S. / Adams, J.J. / Furness, H.S. / Bayer, E.A. / Smith, S.P.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Feb 5, 2020Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: 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: Hyalurononglucosaminidase


Theoretical massNumber of molelcules
Total (without water)15,5101
Polymers15,5101
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)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Hyalurononglucosaminidase / Hyaluronidase / Mu toxin


Mass: 15509.958 Da / Num. of mol.: 1 / Fragment: sequence database residues 1498-1628
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: nagH / Production host: Escherichia coli (E. coli) / References: UniProt: P26831, hyaluronoglucosaminidase

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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 CBCA(CO)NH
1313D HNCO
1413D HN(CA)CB
1513D H(CCO)NH
1613D (H)CCH-TOCSY
1713D HNHA
1813D 1H-13C NOESY
1913D 1H-15N NOESY

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Sample preparation

DetailsContents: 1mM protein, 25 mM HEPES, 50 mM sodium chloride, 5 mM Calclium chloride, 0.5 mM DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMHEPES1
50 mMsodium chloride1
10 %D2O[U-100% 2H]1
5 mMCalclium chloride1
0.5 mMDSS1
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.2.2Johnson, One Moon Scientificdata analysis
NMRView5.2.2Johnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: 1000 molecular dynamic steps
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: 20

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