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- PDB-2bgo: Mannan Binding Module from Man5C -

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Basic information

Entry
Database: PDB / ID: 2bgo
TitleMannan Binding Module from Man5C
ComponentsENDO-B1,4-MANNANASE 5C
KeywordsCARBOHYDRATE BINDING PROTEIN / MANNAN / CARBOHYDRATE BINDING MODULE
Function / homology
Function and homology information


mannan endo-1,4-beta-mannosidase activity / cellulose binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Mannan endo-1,4-beta-mannosidase-like / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate binding module (family 35) / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 ...Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Mannan endo-1,4-beta-mannosidase-like / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate binding module (family 35) / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Carbohydrate binding module family 6 / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-b1,4-mannanase 5C
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodSOLUTION NMR
AuthorsTunnicliffe, R.B. / Bolam, D.N. / Pell, G. / Gilbert, H.J. / Williamson, M.P.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of a Mannan-Specific Family 35 Carbohydrate-Binding Module: Evidence for Significant Conformational Changes Upon Ligand Binding
Authors: Tunnicliffe, R.B. / Bolam, D.N. / Pell, G. / Gilbert, H.J. / Williamson, M.P.
History
DepositionJan 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
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: ENDO-B1,4-MANNANASE 5C


Theoretical massNumber of molelcules
Total (without water)14,9481
Polymers14,9481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 80RANDOM 5 STRUCTURES FROM 20 LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein ENDO-B1,4-MANNANASE 5C / CBM35 FROM BETA-1 / 4-MANNANASE MAN5C


Mass: 14947.636 Da / Num. of mol.: 1 / Fragment: RESIDUES 197-328
Source method: isolated from a genetically manipulated source
Details: MANNAN SPECIFIC CARBOHYDRATE BINDING MODULE / Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Plasmid: PGP1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83 (DE3) / References: UniProt: Q840C0
Sequence detailsPROTEIN SEQUENCE STARTS AT RESIDUE 204 OF FULL LENGTH PROTEIN. ACTUAL PROTEIN SAMPLE CONTAINED ...PROTEIN SEQUENCE STARTS AT RESIDUE 204 OF FULL LENGTH PROTEIN. ACTUAL PROTEIN SAMPLE CONTAINED RESIDUES 197-328 PLUS HIS-TAG SEQUENCE LEHHHHHH AT C-TERMINUS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE EXPERIMENTS
121HNHA
13115N
14113C-EDITED NOESY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 50MM SODIUM PHOSPHATE, 10% D2O
Sample conditionspH: 6 / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Felixstructure solution
CNSstructure solution
NMR ensembleConformer selection criteria: RANDOM 5 STRUCTURES FROM 20 LOWEST ENERGY
Conformers calculated total number: 80 / Conformers submitted total number: 5

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