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- PDB-1e5b: Internal xylan binding domain from C. fimi Xyn10A, R262G mutant -

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Basic information

Entry
Database: PDB / ID: 1e5b
TitleInternal xylan binding domain from C. fimi Xyn10A, R262G mutant
ComponentsXYLANASE D
KeywordsHYDROLASE / XYLAN BINDING DOMAIN / XYLANASE / BETA-SHEET
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / polysaccharide binding / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function
Immunoglobulin-like - #290 / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. ...Immunoglobulin-like - #290 / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Glycoside hydrolase family 11/12 / CBM2/CBM3, carbohydrate-binding domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Bifunctional xylanase/deacetylase
Similarity search - Component
Biological speciesCELLULOMONAS FIMI (bacteria)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING
Model type detailsMINIMIZED AVERAGE
AuthorsSimpson, P.J. / Hefang, X. / Bolam, D.N. / Gilbert, H.J. / Williamson, M.P.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The Structural Basis for the Ligand Specificity of Family 2 Carbohydrate Binding Nodules
Authors: Simpson, P.J. / Hefang, X. / Bolam, D.N. / Gilbert, H.J. / Williamson, M.P.
History
DepositionJul 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XYLANASE D


Theoretical massNumber of molelcules
Total (without water)8,6871
Polymers8,6871
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)1 / 50MINIMISED AVERAGE STRUCTURE
Representative

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Components

#1: Protein XYLANASE D / XBD1 / ENDO-1 / 4-BETA-XYLANASE D


Mass: 8687.275 Da / Num. of mol.: 1 / Fragment: XYLAN BINDING DOMAIN 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLULOMONAS FIMI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83 / References: UniProt: P54865, endo-1,4-beta-xylanase
Compound detailsCHAIN A MUTATION: R262G
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121DQF-COSY
131NOESY
141E.COSY
151HSQC
161NOESY-HMQC
171TOCSY-HMQC
181HNHA
191HNHB
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR NMR SPECTROSCOPY ON A UNIFORMLY 15N-LABELLED SAMPLE OF XBD1 (R262G)

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Sample preparation

DetailsContents: 50MM SODIUM PHOSPHATE, 10MM AZIDE
Sample conditionspH: 5 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Felix97structure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 / Details: YASAP
NMR ensembleConformer selection criteria: MINIMISED AVERAGE STRUCTURE / Conformers calculated total number: 50 / Conformers submitted total number: 1

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