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- PDB-2czn: Solution structure of the chitin-binding domain of hyperthermophi... -

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Basic information

Entry
Database: PDB / ID: 2czn
TitleSolution structure of the chitin-binding domain of hyperthermophilic chitinase from pyrococcus furiosus
Componentschitinase
KeywordsHYDROLASE / chitin binding / pyrococcus furiosus / chitinase
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / polysaccharide binding / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Immunoglobulin-like - #290 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 ...Immunoglobulin-like - #290 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsUegaki, T. / Ikegami, T. / Nakamura, T. / Hagihara, Y. / Mine, S. / Inoue, T. / Matsumura, H. / Ataka, M. / Ishikawa, K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Tertiary structure and carbohydrate recognition by the chitin-binding domain of a hyperthermophilic chitinase from Pyrococcus furiosus.
Authors: Nakamura, T. / Mine, S. / Hagihara, Y. / Ishikawa, K. / Ikegami, T. / Uegaki, K.
History
DepositionJul 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 29, 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: chitinase


Theoretical massNumber of molelcules
Total (without water)10,9641
Polymers10,9641
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)38 / 50structures with the lowest energy, structures with the least restraint violations, structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein chitinase


Mass: 10964.104 Da / Num. of mol.: 1 / Fragment: Chitin binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U1H5, chitinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1233D 13C-separated NOESY
1322D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
1Uniform (random) labeling with 15N90% H2O/10% D2O
2non labeling99% D2O, 1% H2O
3Uniform (random) labeling with 13C, 15N99% D2O, 1% H2O
Sample conditionsIonic strength: 25mM NaCl / pH: 5.6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.841Brungerstructure solution
NMRPipedelaglioprocessing
SparkyGoddard and Knellerdata analysis
X-PLOR3.841refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy, structures with the least restraint violations, structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 38

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