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- PDB-7yhi: Solution structure of O-di-mannosylated carbohydrate binding modu... -

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Basic information

Entry
Database: PDB / ID: 7yhi
TitleSolution structure of O-di-mannosylated carbohydrate binding module (CBM) of the glycoside hydrolase Family 7 cellobiohydrolase from Trichoderma reesei
ComponentsExoglucanase 1
KeywordsHYDROLASE / CARBOHYDRATE BINDING
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesTrichoderma reesei (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, C. / Feng, Y. / Tan, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070125 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural insight into why S-linked glycosylation cannot adequately mimic the role of natural O-glycosylation.
Authors: Chen, C. / Ma, B. / Wang, Y. / Cui, Q. / Yao, L. / Li, Y. / Chen, B. / Feng, Y. / Tan, Z.
History
DepositionJul 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 13, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exoglucanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0882
Polymers3,7461
Non-polymers3421
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area450 Å2
ΔGint7 kcal/mol
Surface area2490 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Exoglucanase 1 / 1 / 4-beta-cellobiohydrolase / Exocellobiohydrolase I / CBHI / Exoglucanase I


Mass: 3746.126 Da / Num. of mol.: 1 / Fragment: UNP residues 478-513 / Source method: obtained synthetically / Source: (synth.) Trichoderma reesei (fungus)
References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
Has ligand of interestY
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-1H TOCSY
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-13C HSQC-TOCSY
161isotropic12D 1H-15N HSQC
172isotropic12D 1H-1H TOCSY
182isotropic12D 1H-1H COSY
192isotropic12D 1H-1H NOESY
1102isotropic12D 1H-13C HSQC
1112isotropic12D 1H-13C HSQC-TOCSY
1122isotropic12D 1H-13C H2BC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution14 mg/mL CBM020, 50 mM [U-100% 2H] sodium acetate, 0.01 % w/v DSS, 90% H2O/10% D2OH2Osample90% H2O/10% D2O
solution24 mg/mL CBM020, 50 mM [U-100% 2H] sodium acetate, 0.01 % w/v DSS, 100% D2OD2Osample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mg/mLCBM020natural abundance1
50 mMsodium acetate[U-100% 2H]1
0.01 % w/vDSSnatural abundance1
4 mg/mLCBM020natural abundance2
50 mMsodium acetate[U-100% 2H]2
0.01 % w/vDSSnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: condition1 / pH: 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: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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