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- PDB-1k45: The Solution Structure of the CBM4-2 Carbohydrate Binding Module ... -

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Basic information

Entry
Database: PDB / ID: 1k45
TitleThe Solution Structure of the CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase.
ComponentsXylanase
KeywordsHYDROLASE / beta-sandwich formed by 11 strands. Binding-site cleft. Solvent exposed aromatics (Trp69 / Phe110) in binding cleft. Two helical twists. Two calcium binding sites.
Function / homology
Function and homology information


endo-1,4-beta-xylanase / xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Secretion system C-terminal sorting domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodSOLUTION NMR / hybrid distance geometry, simulated annealing using XPLOR
Model type detailsminimized average
AuthorsSimpson, P.J. / Jamieson, S.J. / Abou-Hachem, M. / Nordberg-Karlsson, E. / Gilbert, H.J. / Holst, O. / Williamson, M.P.
CitationJournal: Biochemistry / Year: 2002
Title: The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase.
Authors: Simpson, P.J. / Jamieson, S.J. / Abou-Hachem, M. / Karlsson, E.N. / Gilbert, H.J. / Holst, O. / Williamson, M.P.
History
DepositionOct 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)18,1041
Polymers18,1041
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 / -
Representativeminimized average structure

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Components

#1: Protein Xylanase


Mass: 18103.803 Da / Num. of mol.: 1
Fragment: Second family 4 carbohydrate binding module (CBM4-2)(Residues 211-373)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (bacteria) / Gene: xyn10A / Plasmid: pET-25b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P96988, 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
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA

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Sample preparation

DetailsContents: 1.5 mM CBM4-2 15N-labelled, and 13C,15N double labelled protein; 50 mM CaCl2, 50 mM sodium acetate-d3, pH 6.0, 10% D2O, 10 mM sodium azide, 0.1 mM sodium trimethylsilylpropionate (TSP)
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.2 M / pH: 6 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000Molecular Simulations Inc.processing
X-PLOR3.1Axel T. Brungerstructure solution
X-PLOR3.1Axel T. Brungerrefinement
RefinementMethod: hybrid distance geometry, simulated annealing using XPLOR
Software ordinal: 1
Details: The final set of restraints contained 1654 non-redundant unambiguous NOEs and 17 ambiguous NOEs, 93 dihedral angle restraints, 72 chi1 and 1 chi2 restraint, and 65 pairs of hydrogen bond ...Details: The final set of restraints contained 1654 non-redundant unambiguous NOEs and 17 ambiguous NOEs, 93 dihedral angle restraints, 72 chi1 and 1 chi2 restraint, and 65 pairs of hydrogen bond restraints, plus 177 backbone dihedral restraints based on 13C shifts from TALOS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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