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- PDB-5yzk: Solution structure of LysM domain from a chitinase derived from V... -

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Basic information

Entry
Database: PDB / ID: 5yzk
TitleSolution structure of LysM domain from a chitinase derived from Volvox carteri
ComponentsChitinase, lysozyme
KeywordsHYDROLASE / lysin motif / chitin-specific / CBM50 / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / LysM domain superfamily / Lysin motif / LysM domain / LysM domain profile. / LysM domain / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesVolvox carteri f. nagariensis (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsKitaoku, Y. / Nishimura, S. / Fukamizo, T. / Ohnuma, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS16J10483 Japan
CitationJournal: Glycobiology / Year: 2019
Title: Structures and chitin-binding properties of two N-terminal lysin motifs (LysMs) found in a chitinase from Volvox carteri.
Authors: Kitaoku, Y. / Nishimura, S. / Hirono, T. / Suginta, W. / Ohnuma, T. / Fukamizo, T.
History
DepositionDec 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase, lysozyme


Theoretical massNumber of molelcules
Total (without water)5,2901
Polymers5,2901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3530 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Chitinase, lysozyme / LysM


Mass: 5290.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Volvox carteri f. nagariensis (plant) / Gene: chi4, VOLCADRAFT_127242 / Production host: Escherichia coli (E. coli) / References: UniProt: D8UFB5
Has protein modificationY

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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 HNCO
131isotropic13D HN(CA)CO
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
1122isotropic13D 1H-15N NOESY
1112isotropic13D 1H-15N TOCSY
1142isotropic13D HBHACBCACONH
2103isotropic12D 1H-13C HSQC
293isotropic13D 1H-13C NOESY aliphatic
283isotropic13D 1H-13C NOESY aromatic
273isotropic13D (H)CCH-TOCSY
263isotropic13D CCH-TOCSY
2133isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1194 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 90% H2O/10% D2O13C,15N_sample_190% H2O/10% D2O
solution2359 uM [U-13C; U-15N] LysM, 20 mM [U-13C; U-15N] sodium acetate, 100% D2O13C,15N_sample_2100% D2O
solution3287 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O13C,15N_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
194 uMLysM[U-13C; U-15N]1
20 mMsodium acetate[U-2H]1
359 uMLysM[U-13C; U-15N]2
20 mMsodium acetate[U-13C; U-15N]2
287 uMLysM[U-13C; U-15N]3
20 mMsodium acetate[U-2H]3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mM13C,15N_sample_H2O51 atm300 K
220 mM13C,15N_sample_D2O51 atm300 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / 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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