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- PDB-1hej: C-terminal xylan binding domain from Cellulomonas fimi xylanase 11A -

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Basic information

Entry
Database: PDB / ID: 1hej
TitleC-terminal xylan binding domain from Cellulomonas fimi xylanase 11A
ComponentsENDO-1,4-BETA-XYLANASE D
KeywordsHYDROLASE(XYLAN DEGRADATION) / HYDROLASE / 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. / Hefang, X. / Bolam, D.N. / White, P. / Hancock, S.M. / Gilbert, H.J. / Williamson, M.P.
CitationJournal: Biochemistry / Year: 2001
Title: Evidence for Synergy between Family 2B Carbohydrate Binding Modules in Cellulomonas Fimi Xylanase 11A
Authors: Bolam, D.N. / Xie, H. / White, P. / Simpson, P.J. / Hancock, S.M. / Williamson, M.P. / Gilbert, H.J.
History
DepositionNov 22, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: ENDO-1,4-BETA-XYLANASE D


Theoretical massNumber of molelcules
Total (without water)8,7501
Polymers8,7501
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 23 LOWEST ENERGY STRUCTURES
Representative

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE D / XYLANASE D / CBM2B-2 / XBD2


Mass: 8750.339 Da / Num. of mol.: 1 / Fragment: XYLAN BINDING DOMAIN 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLULOMONAS FIMI (bacteria) / Strain: JM83 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54865, endo-1,4-beta-xylanase
Compound detailsENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS. BELONGS TO CELLULASE FAMILY G (FAMILY 11 ...ENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS. BELONGS TO CELLULASE FAMILY G (FAMILY 11 OF GLYCOSYL HYDROLASES).

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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 XBD2

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Sample preparation

DetailsContents: SODIUM PHOSPHATE 50 MM, SODIUM AZIDE 10 MM
Sample conditionspH: 5.0 / Temperature: 303 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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
MSI FELIX97structure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 / Details: YASAP PROTOCOL. DETAILS IN THE JRNL CITATION.
NMR ensembleConformer selection criteria: RANDOM SELECTION OF 5 FROM THE 23 LOWEST ENERGY STRUCTURES
Conformers calculated total number: 50 / Conformers submitted total number: 5

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