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- PDB-1xbd: INTERNAL XYLAN BINDING DOMAIN FROM CELLULOMONAS FIMI XYLANASE D, ... -

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Basic information

Entry
Database: PDB / ID: 1xbd
TitleINTERNAL XYLAN BINDING DOMAIN FROM CELLULOMONAS FIMI XYLANASE D, NMR, 5 STRUCTURES
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 activity / endo-1,4-beta-xylanase / 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
AuthorsSimpson, P.J. / Bolam, D.N. / Cooper, A. / Ciruela, A. / Hazlewood, G.P. / Gilbert, H.J. / Williamson, M.P.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.
Authors: Simpson, P.J. / Bolam, D.N. / Cooper, A. / Ciruela, A. / Hazlewood, G.P. / Gilbert, H.J. / Williamson, M.P.
History
DepositionOct 16, 1998Processing site: BNL
Revision 1.0Jul 21, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XYLANASE D


Theoretical massNumber of molelcules
Total (without water)8,7871
Polymers8,7871
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)5 / 50RANDOM SELECTION OF 5 FROM THE 38 LOWEST ENERGY STRUCTURES
Representative

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Components

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


Mass: 8787.418 Da / Num. of mol.: 1 / Fragment: XYLAN BINDING DOMAIN 1
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

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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

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Sample preparation

Sample conditionspH: 5.0 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX500BrukerDRX5005001
Bruker DRX600BrukerDRX6006002
Bruker DRX800BrukerDRX8008003

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
MSI FELIX97structure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 / Details: YASAP
NMR ensembleConformer selection criteria: RANDOM SELECTION OF 5 FROM THE 38 LOWEST ENERGY STRUCTURES
Conformers calculated total number: 50 / Conformers submitted total number: 5

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