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- PDB-6z40: NMR solution structure of the carbohydrate-binding module family ... -

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Basic information

Entry
Database: PDB / ID: 6z40
TitleNMR solution structure of the carbohydrate-binding module family 5 (CBM5) from Cellvibrio japonicus CjLPMO10A
ComponentsCarbohydrate binding protein, putative, cpb33A
KeywordsSUGAR BINDING PROTEIN / cbm / chitin
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Immunoglobulin E-set
Similarity search - Domain/homology
Carbohydrate binding protein, putative, cpb33A
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsMadland, E. / Aachmann, F.L. / Courtade, G.
Funding support Norway, Denmark, 3items
OrganizationGrant numberCountry
Research Council of Norway269408 Norway
Research Council of Norway226244 Norway
Novo Nordisk FoundationNNF18OC0032242 Denmark
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus.
Authors: Madland, E. / Forsberg, Z. / Wang, Y. / Lindorff-Larsen, K. / Niebisch, A. / Modregger, J. / Eijsink, V.G.H. / Aachmann, F.L. / Courtade, G.
#1: Journal: Biorxiv / Year: 2021
Title: NMR structures and functional roles of two related chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus
Authors: Madland, E. / Forsberg, Z. / Wang, Y. / Lindorff-Larsen, K. / Niebisch, A. / Modregger, J. / Eijsink, V.G.H. / Aachmann, F.L. / Courtade, G.
History
DepositionMay 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: citation / pdbx_database_status
Item: _citation.journal_id_ISSN / _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: Carbohydrate binding protein, putative, cpb33A


Theoretical massNumber of molelcules
Total (without water)7,6301
Polymers7,6301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Carbohydrate binding protein, putative, cpb33A


Mass: 7630.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus (strain Ueda107) (bacteria)
Gene: cbp33A, CJA_2191 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3PJ79

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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
122isotropic13D HNCA
132isotropic13D HN(CO)CA
142isotropic13D HNCO
152isotropic13D CBCA(CO)NH
162isotropic12D 1H-13C HSQC aliphatic
172isotropic12D 1H-13C HSQC aromatic
182isotropic13D (H)CCH-TOCSY
192isotropic13D 1H-13C NOESY aliphatic
1102isotropic13D 1H-13C NOESY aromatic
1111isotropic13D 1H-15N NOESY
1123isotropic12D 1H-1H NOESY
1132isotropic13D HN(CA)CO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.1 mM [U-15N] CBM5, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.1 mM [U-13C; U-15N] CBM5, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O13C_sample90% H2O/10% D2O
solution30.1 mM CBM5, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2Ona_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMCBM5[U-15N]1
25 mMsodium phosphatenatural abundance1
10 mMsodium chloridenatural abundance1
0.1 mMCBM5[U-13C; U-15N]2
25 mMsodium phosphatenatural abundance2
10 mMsodium chloridenatural abundance2
0.1 mMCBM5natural abundance3
25 mMsodium phosphatenatural abundance3
10 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 55 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
TopSpin3.5Bruker Biospinprocessing
CARA1.5.5Keller and Wuthrichchemical shift assignment
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
YASARA14.6.23Elmar Krieger, Keehyoung Joo, Jinwoo Lee,3 Jooyoung Lee, Srivatsan Raman, James Thompson, Mike Tyka, David Baker, and Kevin Karplusrefinement
Refinement
MethodSoftware ordinal
simulated annealing5
molecular dynamics3
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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