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- PDB-2lro: Solution structure, dynamics and binding studies of CtCBM11 -

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Basic information

Entry
Database: PDB / ID: 2lro
TitleSolution structure, dynamics and binding studies of CtCBM11
ComponentsEndoglucanase H
KeywordsHYDROLASE / Cellulosome
Function / homology
Function and homology information


cellulase / beta-glucosidase activity / cellulase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Galactose-binding lectin / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. ...Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Galactose-binding lectin / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / EF-hand calcium-binding domain. / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium thermocellum (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 17
AuthorsViegas, A. / Cabrita, E.J.
CitationJournal: Biochem.J. / Year: 2013
Title: Solution structure, dynamics and binding studies of a family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11).
Authors: Viegas, A. / Sardinha, J. / Freire, F. / Duarte, D.F. / Carvalho, A.L. / Fontes, C.M. / Romao, M.J. / Macedo, A.L. / Cabrita, E.J.
History
DepositionApr 11, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0433
Polymers18,9631
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 / 20target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Endoglucanase H / Cellulase H / Endo-1 / 4-beta-glucanase H / EgH


Mass: 18963.096 Da / Num. of mol.: 1 / Fragment: CBM11 domain residues 655-821
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: celH, Cthe_1472 / Production host: Escherichia coli (E. coli) / References: UniProt: P16218, cellulase
#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 HNCO
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HNHA
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY
11013D 1H-13C NOESY aromatic
11113D 1H-15N NOESY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] protein_1, 0.75 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-13C; U-15N]1
0.75 mMpotassium phosphate-21
Sample conditionsIonic strength: 0.75 / pH: 7.5 / 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
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
TopSpin2.1Bruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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