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- PDB-1qld: Solution structure of type X CBM -

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Basic information

Entry
Database: PDB / ID: 1qld
TitleSolution structure of type X CBM
ComponentsXYLANASE
KeywordsXYLANASE / BETA STRANDS / ANTI PARALLEL BETA SHEETS / XYLAN DEGRADATION / HYDROLASE / GLYCOSIDASE
Function / homology
Function and homology information


cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Xylanase; Chain A / CBM10 / Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. ...Xylanase; Chain A / CBM10 / Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
Model type detailsMINIMIZED AVERAGE
AuthorsRaghothama, S. / Simpson, P.J. / Gilbert, H.J. / Williamson, M.P.
CitationJournal: Biochemistry / Year: 2000
Title: Solution Structure of Cbm10 Cellulose Binding Module from Pseudomonas Xylanase A
Authors: Raghothama, S. / Simpson, P.J. / Szabo, L. / Nagy, T. / Gilbert, H.J. / Williamson, M.P.
History
DepositionAug 26, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2000Provider: 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 / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XYLANASE


Theoretical massNumber of molelcules
Total (without water)5,4001
Polymers5,4001
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)1 / 50AN AVERAGE STRUCTURE OF 21 LOWEST ENERGY STRUCTURES WAS CALCULATED, WHICH WAS FURTHER SUBJECTED TO RESTRAINED ENERGY MINIMIZATION.
Representative

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Components

#1: Protein/peptide XYLANASE / / ENDO-1 / 4-BETA-XYLANASE A / XYLANASE A / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE A


Mass: 5400.007 Da / Num. of mol.: 1 / Fragment: CELLULOSE BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Description: PSEUDOMONAS FLUORESCENS CELLULOSA / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P14768, 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
121NOESY
131DQF-COSY
141E.COSY
NMR detailsText: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. FOR THE ATOM RECORDS THE VALUE GIVEN IN THE TEMPERATURE FACTOR COLUMN IS THE RMSD PER ATOM TO THE MEAN POSITION.

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Sample preparation

DetailsContents: 90% WATER / 10% D2O
Sample conditionsIonic strength: 100 MM NACL / pH: 4.5 / Pressure: AMBIENT / Temperature: 323 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
FELIXstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: AN AVERAGE STRUCTURE OF 21 LOWEST ENERGY STRUCTURES WAS CALCULATED, WHICH WAS FURTHER SUBJECTED TO RESTRAINED ENERGY MINIMIZATION.
Conformers calculated total number: 50 / Conformers submitted total number: 1

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