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- PDB-6twe: Cu(I) NMR solution structure of the chitin-active lytic polysacch... -

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Basic information

Entry
Database: PDB / ID: 6twe
TitleCu(I) NMR solution structure of the chitin-active lytic polysaccharide monooxygenase BlLPMO10A
ComponentsPutative chitin binding protein
KeywordsOXIDOREDUCTASE / lytic polysaccharide monooxygenase / lpmo / AA10 / Chitin / copper
Function / homologyCellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set / COPPER (I) ION / Putative chitin binding protein
Function and homology information
Biological speciesBacillus licheniformis DSM 13 = ATCC 14580 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsCourtade, G. / Wimmer, R. / Aachmann, F.L.
Funding support Norway, Denmark, 5items
OrganizationGrant numberCountry
Norwegian Research Council221576 Norway
Norwegian Research Council226244 Norway
Other privateObel Foundation Denmark
Other privateSparNord Foundation Denmark
The Carlsberg Foundation Denmark
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Mechanistic basis of substrate-O2coupling within a chitin-active lytic polysaccharide monooxygenase: An integrated NMR/EPR study.
Authors: Courtade, G. / Ciano, L. / Paradisi, A. / Lindley, P.J. / Forsberg, Z. / Sorlie, M. / Wimmer, R. / Davies, G.J. / Eijsink, V.G.H. / Walton, P.H. / Aachmann, F.L.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 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:
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Assembly

Deposited unit
A: Putative chitin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2592
Polymers19,1951
Non-polymers641
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11710 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Putative chitin binding protein


Mass: 19195.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis DSM 13 = ATCC 14580 (bacteria)
Gene: chbB, BL00145 / Production host: Escherichia coli (E. coli) / Variant (production host): RV308 / References: UniProt: Q62YN7
#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu

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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
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D HNCA
141isotropic12D 1H-13C HSQC aromatic
151isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY aliphatic
171isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.1 mM [U-98% 13C; U-98% 15N] BlLPMO10A, 20 mM MES, 1 saturated Cu(I)Cl, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMBlLPMO10A[U-98% 13C; U-98% 15N]1
20 mMMESnatural abundance1
1 saturatedCu(I)Clnatural abundance1
Sample conditionsDetails: Incubated for 48h in anoxic environment, added Cu(I)Cl and sealed the tube.
Ionic strength: 20 mM / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K

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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
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
YASARA14.6.23Krieger, Darden, Nabuurs, Finkelstein, Vriendrefinement
CARA1.5.5Keller and Wuthrichdata analysis
XEASYBartels et al.data analysis
TopSpin3.5Bruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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