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- PDB-2l8a: Structure of a novel CBM3 lacking the calcium-binding site -

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Basic information

Entry
Database: PDB / ID: 2l8a
TitleStructure of a novel CBM3 lacking the calcium-binding site
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / carbohydrate-binding module / family 3
Function / homology
Function and homology information


glucan catabolic process / cellulose binding / cellulase / beta-glucosidase activity / cellulase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Endoglucanase-like / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 ...Endoglucanase-like / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsPaiva, J.H. / Meza, A.N. / Sforca, M.L. / Navarro, R.Z. / Neves, J.L. / Santos, C.R. / Murakami, M.T. / Zeri, A.C.
CitationJournal: Biochem.J. / Year: 2012
Title: Dissecting structure-function-stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168.
Authors: Santos, C.R. / Paiva, J.H. / Sforca, M.L. / Neves, J.L. / Navarro, R.Z. / Cota, J. / Akao, P.K. / Hoffmam, Z.B. / Meza, A.N. / Smetana, J.H. / Nogueira, M.L. / Polikarpov, I. / Xavier-Neto, ...Authors: Santos, C.R. / Paiva, J.H. / Sforca, M.L. / Neves, J.L. / Navarro, R.Z. / Cota, J. / Akao, P.K. / Hoffmam, Z.B. / Meza, A.N. / Smetana, J.H. / Nogueira, M.L. / Polikarpov, I. / Xavier-Neto, J. / Squina, F.M. / Ward, R.J. / Ruller, R. / Zeri, A.C. / Murakami, M.T.
History
DepositionJan 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)16,7181
Polymers16,7181
Non-polymers00
Water0
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 least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Endoglucanase / Cellulase / Carboxymethyl-cellulase / CMCase / Cellulase / Endo-1 / 4-beta-glucanase


Mass: 16717.598 Da / Num. of mol.: 1 / Fragment: CBM3 domain residues 354-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: eglS, bglC, gld, BSU18130 / Production host: Escherichia coli (E. coli) / References: UniProt: P10475, cellulase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1422D 1H-13C HSQC
1533D (H)CCH-TOCSY
1633D 1H-13C NOESY
1713D 1H-15N NOESY
1813D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-99% 15N] cbm, 95% H2O/5% D2O95% H2O/5% D2O
20.3 mM [U-100% 13C; U-100% 15N] cbm, 95% H2O/5% D2O95% H2O/5% D2O
30.3 mM [U-100% 13C; U-100% 15N] cbm, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMcbm-1[U-99% 15N]1
0.3 mMcbm-2[U-100% 13C; U-100% 15N]2
0.3 mMcbm-3[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 70 / pH: 7.2 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificchemical shift assignment
NMRView5Johnson, One Moon Scientificchemical shift calculation
NMRView5Johnson, One Moon Scientificpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANArefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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