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- PDB-6f7e: NMR solution structure of the cellulose-binding family 2 carbohyd... -

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Basic information

Entry
Database: PDB / ID: 6f7e
TitleNMR solution structure of the cellulose-binding family 2 carbohydrate binding domain (CBM2) from ScLPMO10C
ComponentsPutative secreted cellulose binding protein
KeywordsCARBOHYDRATE / cellulose binding / beta-sandwich fold / lytic polysaccharide monooxgynease / lpmo
Function / homology
Function and homology information


xyloglucan metabolic process / polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Secreted cellulose binding protein
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodSOLUTION NMR / molecular dynamics
AuthorsCourtade, G. / Forsberg, Z. / Eijsink, V. / Aachmann, F.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway221576 Norway
Research Council of Norway226244 Norway
Citation
Journal: J.Biol.Chem. / Year: 2018
Title: The carbohydrate-binding module and linker of a modular lytic polysaccharide monooxygenase promote localized cellulose oxidation.
Authors: Courtade, G. / Forsberg, Z. / Heggset, E.B. / Eijsink, V.G.H. / Aachmann, F.L.
#1: Journal: Biomol NMR Assign / Year: 2017
Title: Chemical shift assignments for the apo-form of the catalytic domain, the linker region, and the carbohydrate-binding domain of the cellulose-active lytic polysaccharide monooxygenase ScLPMO10C.
Authors: Courtade, G. / Forsberg, Z. / Vaaje-Kolstad, G. / Eijsink, V.G.H. / Aachmann, F.L.
History
DepositionDec 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: 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: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jan 29, 2020Group: Database references / Category: database_2
Revision 1.4Dec 7, 2022Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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 secreted cellulose binding protein


Theoretical massNumber of molelcules
Total (without water)10,6631
Polymers10,6631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6290 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256target function
RepresentativeModel #1target function

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Components

#1: Protein Putative secreted cellulose binding protein


Mass: 10662.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO1188 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RJY2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
123isotropic22D 1H-13C HSQC aliphatic
132isotropic12D 1H-13C HSQC aromatic
141isotropic23D HNHA
153isotropic23D HNCO
163isotropic23D HN(CA)CO
173isotropic23D HNCA
183isotropic23D HN(COCA)CB
193isotropic23D (H)CCH-TOCSY
1102isotropic22D CACO
1113isotropic22D CON
1121isotropic13D 1H-15N NOESY
1132isotropic13D 1H-15N NOESY aliphatic
1142isotropic13D 1H-15N NOESY aromatic
1154isotropic12D COSY
1164isotropic12D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution125 mM sodium phosphate, 25 mM sodium chloride, 0.5 mM [U-98% 15N] ScCBM2, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution225 mM sodium phosphate, 25 mM sodium chloride, 0.5 mM [U-98% 13C; U-98% 15N] ScCBM2, 100% D2O13C15N_sample_D2O100% D2O
solution325 mM sodium phosphate, 25 mM sodium chloride, 0.5 mM [U-98% 13C; U-98% 15N] ScCBM2, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution425 mM sodium phosphate, 25 mM sodium chloride, 0.5 mM ScCBM2, 100% D2Ona_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphatenatural abundance1
25 mMsodium chloridenatural abundance1
0.5 mMScCBM2[U-98% 15N]1
25 mMsodium phosphatenatural abundance2
25 mMsodium chloridenatural abundance2
0.5 mMScCBM2[U-98% 13C; U-98% 15N]2
25 mMsodium phosphatenatural abundance3
25 mMsodium chloridenatural abundance3
0.5 mMScCBM2[U-98% 13C; U-98% 15N]3
25 mMsodium phosphatenatural abundance4
25 mMsodium chloridenatural abundance4
0.5 mMScCBM2natural abundance4
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III80015 mm Z-gradient CP-TCI (H/C/N) probe
Bruker AVANCE IIIBrukerAVANCE III60025 mm Z-gradient CP-TCI (H/C/N) probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospinprocessing
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.5Keller and Wuthrichchemical shift assignment
YASARA14.6.23Elmar Kriegerrefinement
MddNMR2Orekhov, Jaravine, Mayzel and Kazimierczukprocessing
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 256 / Conformers submitted total number: 20

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