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- PDB-5lw4: NMR solution structure of the apo-form of the chitin-active lytic... -

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Basic information

Entry
Database: PDB / ID: 5lw4
TitleNMR solution structure of the apo-form of the chitin-active lytic polysaccharide monooxygenase BlLPMO10A
ComponentsPutative chitin binding protein
KeywordsOXIDOREDUCTASE / lytic polysaccharide monooxygenase / lpmo / AA10 / Chitin / Cellulose
Function / homologyCellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set / Putative chitin binding protein
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsCourtade, G. / Wimmer, R. / Aachmann, F.L.
Funding support Norway, Denmark, 5items
OrganizationGrant numberCountry
Research Council of Norway221576 Norway
Research Council of Norway226244 Norway
Obel Foundation Denmark
Spar Nord Foundation Denmark
Carlsberg Foundation Denmark
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Mechanistic basis of substrate-O2 coupling within a chitin-active lytic polysaccharide monooxygenase: an integrated NMR/EPR study
Authors: Courtade, G. / Ciano, L. / Paradisi, A. / Lindley, P. / Forsberg, Z. / Sorlie, M. / Wimmer, R. / Davies, G.J. / Eijsink, V.G.H. / Walton, P.H. / Aachmann, F.L.
History
DepositionSep 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jan 22, 2020Group: Data collection / Database references / Category: pdbx_database_related / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3Jul 29, 2020Group: Author supporting evidence / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_audit_support.funding_organization / _struct.title
Revision 1.4Jun 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: Putative chitin binding protein


Theoretical massNumber of molelcules
Total (without water)19,1951
Polymers19,1951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11430 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 259target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Putative chitin binding protein


Mass: 19195.395 Da / Num. of mol.: 1 / Fragment: UNP residues 32-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: chbB, BL00145 / Production host: Escherichia coli (E. coli) / Variant (production host): RV308 / References: UniProt: Q62YN7

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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
122isotropic12D 1H-13C HSQC aliphatic
132isotropic12D 1H-13C HSQC aromatic
142isotropic13D HNCO
152isotropic13D HN(CA)CO
162isotropic13D HNCA
192isotropic13D CBCANH
182isotropic13D CBCA(CO)NH
172isotropic13D HBHA(CO)NH
1103isotropic13D (H)CCH-TOCSY
1113isotropic12D (HB)CB(CGCD)HD
1123isotropic12D CACO
1133isotropic12D CON
1141isotropic13D 1H-15N NOESY
1152isotropic23D 1H-15N NOESY
1162isotropic13D 1H-13C NOESY aliphatic
1172isotropic13D 1H-13C NOESY aromatic
1182isotropic23D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-98% 15N] BlLPMO10A, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.8 mM [U-98% 13C; U-98% 15N] BlLPMO10A, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution30.8 mM [U-98% 13C; U-98% 15N] BlLPMO10A, 25 mM sodium phosphate, 10 mM sodium chloride, 100% D2O13C_15N_D2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMBlLPMO10A[U-98% 15N]1
25 mMsodium phosphatenatural abundance1
10 mMsodium chloridenatural abundance1
0.8 mMBlLPMO10A[U-98% 13C; U-98% 15N]2
25 mMsodium phosphatenatural abundance2
10 mMsodium chloridenatural abundance2
0.8 mMBlLPMO10A[U-98% 13C; U-98% 15N]3
25 mMsodium phosphatenatural abundance3
10 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 35 mM / Label: conditions_1 / pH: 5.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AscendBrukerAscend8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
YASARA14.6.23Krieger, Darden, Nabuurs, Finkelstein, Vriendrefinement
CARA1.9.0Keller and Wuthrichdata analysis
XEASYBartels et al.data analysis
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 259 / Conformers submitted total number: 20

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