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- PDB-2mte: Solution structure of Doc48S -

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Basic information

Entry
Database: PDB / ID: 2mte
TitleSolution structure of Doc48S
ComponentsCellulose 1,4-beta-cellobiosidase (reducing end) CelS
KeywordsHYDROLASE / Calcium-binding protein
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (reducing end) / cellulose 1,4-beta-cellobiosidase activity (reducing end) / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Type 1 dockerin domain / Dockerin domain / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain ...Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Type 1 dockerin domain / Dockerin domain / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cellulose 1,4-beta-cellobiosidase (reducing end) CelS
Similarity search - Component
Biological speciesRuminiclostridium thermocellum (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsChen, C. / Feng, Y.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Revisiting the NMR solution structure of the Cel48S type-I dockerin module from Clostridium thermocellum reveals a cohesin-primed conformation.
Authors: Chen, C. / Cui, Z. / Xiao, Y. / Cui, Q. / Smith, S.P. / Lamed, R. / Bayer, E.A. / Feng, Y.
History
DepositionAug 18, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 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: Cellulose 1,4-beta-cellobiosidase (reducing end) CelS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7513
Polymers7,6711
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cellulose 1,4-beta-cellobiosidase (reducing end) CelS / Cellobiohydrolase CelS / Cellulase SS / Endo-1 / 4-beta-glucanase / Endoglucanase SS / EGSS / Exocellulase


Mass: 7670.523 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 673-741
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum (bacteria)
Gene: celS / Production host: Escherichia coli (E. coli)
References: UniProt: P0C2S5, cellulose 1,4-beta-cellobiosidase (reducing end)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CA)CO
1713D HBHA(CO)NH
1813D HBHANH
1913D (H)CCH-TOCSY
11013D CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.3-0.5 mM [U-13C; U-15N] entity_1-1, 50 mM Bis-Tris-2, 100 mM potassium chloride-3, 20 mM CaCl2-4, 0.02 % w/v DSS-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-13C; U-15N]0.3-0.51
50 mMBis-Tris-21
100 mMpotassium chloride-31
20 mMCaCl2-41
0.02 w/vDSS-51
Sample conditionsIonic strength: 150 / pH: 6.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, molecular dynamics / 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 / Representative conformer: 1

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