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- PDB-6ffu: Solution NMR structure of CBM64 from S.thermophila using 20% 13C,... -

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Basic information

Entry
Database: PDB / ID: 6ffu
TitleSolution NMR structure of CBM64 from S.thermophila using 20% 13C, 100% 15N
ComponentsGlycosyl hydrolase family 5 cellulase CBM64
KeywordsSUGAR BINDING PROTEIN / CBM64
Function / homology
Function and homology information


cellulase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Carbohydrate-binding module 64 / Carbohydrate-binding module 64 / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesSpirochaeta thermophila (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHeikkinen, H.A. / Iwai, H.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland# 1277335 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Molecules / Year: 2021
Title: NMR Structure Determinations of Small Proteins Using only One Fractionally 20% 13 C- and Uniformly 100% 15 N-Labeled Sample.
Authors: Heikkinen, H.A. / Backlund, S.M. / Iwai, H.
History
DepositionJan 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Feb 10, 2021Group: 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_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.3Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Jun 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
Revision 1.5Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase family 5 cellulase CBM64


Theoretical massNumber of molelcules
Total (without water)10,0261
Polymers10,0261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5220 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Glycosyl hydrolase family 5 cellulase CBM64 / carbohydrate binding module 64


Mass: 10025.756 Da / Num. of mol.: 1
Fragment: C-terminal 86-residue module of CBM64 from S.thermophila, UNP residues 456-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirochaeta thermophila (bacteria) / Gene: STHERM_c20620 / Production host: Escherichia coli (E. coli) / References: UniProt: E0RQU0

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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
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HN(CA)CB
161isotropic13D CBCA(CO)NH
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY
191isotropic13D 1H-15N TOCSY
1101isotropic13D (H)CCH-COSY

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Sample preparation

DetailsType: solution
Contents: 9.85 mg/mL 20% 13C, 100% 15N CBM64_20C13, 95% H2O/5% D2O
Details: NMR sample / Label: 13C_20%_15N_100% / Solvent system: 95% H2O/5% D2O
SampleConc.: 9.85 mg/mL / Component: CBM64_20C13 / Isotopic labeling: 20% 13C, 100% 15N
Sample conditionsIonic strength: 20 mM / Label: conditions_20 / pH: 6 / Pressure: 1 bar / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz / Details: HD

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
PSVS1.5Bhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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