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- PDB-5x36: Solution structure of the Family 1 carbohydrate-binding module wi... -

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Basic information

Entry
Database: PDB / ID: 5x36
TitleSolution structure of the Family 1 carbohydrate-binding module with mannosylated Ser3
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
alpha-D-mannopyranose / Exoglucanase 1
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsFeng, Y. / Tan, Z.
Funding support United States, China, 4items
OrganizationGrant numberCountry
the NSF CAREER AwardCHE-1454925 United States
the National Natural Science Foundation of China31270784 China
the National Natural Science Foundation of China31670735 China
Chinese Government Scholarship201604910035 China
CitationJournal: Biochemistry / Year: 2017
Title: Structural Insight into the Stabilizing Effect of O-Glycosylation
Authors: Chaffey, P.K. / Guan, X. / Chen, C. / Ruan, Y. / Wang, X. / Tran, A.H. / Koelsch, T.N. / Cui, Q. / Feng, Y. / Tan, Z.
History
DepositionFeb 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jun 14, 2023Group: Database references / Other / Structure summary / Category: chem_comp / database_2 / pdbx_database_status
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exoglucanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9262
Polymers3,7461
Non-polymers1801
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area190 Å2
ΔGint2 kcal/mol
Surface area2470 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.) Hypocrea jecorina (fungus)
References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
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 DQF-COSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-13C HSQC-TOCSY
161isotropic12D 1H-15N HSQC
172isotropic12D 1H-1H TOCSY
182isotropic12D DQF-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
solution15 mg/mL CBM, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 90% H2O/10% D2Ocbm-h2o90% H2O/10% D2O
solution25 mg/mL CBM, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 100% D2Ocbm-d2o100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mg/mLCBMnatural abundance1
50 mMsodium acetate[U-2H]1
0.1 mg/mLDSSnatural abundance1
5 mg/mLCBMnatural abundance2
50 mMsodium acetate[U-2H]2
0.1 mg/mLDSSnatural 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
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
SANEDuggan, Legge, Dyson & Wrightstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
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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