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- PDB-1ed7: SOLUTION STRUCTURE OF THE CHITIN-BINDING DOMAIN OF BACILLUS CIRCU... -

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Entry
Database: PDB / ID: 1ed7
TitleSOLUTION STRUCTURE OF THE CHITIN-BINDING DOMAIN OF BACILLUS CIRCULANS WL-12 CHITINASE A1
ComponentsCHITINASE A1
KeywordsHYDROLASE / twisted beta-sandwich
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Carbohydrate-binding module superfamily 5/12 / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : ...Carbohydrate-binding module superfamily 5/12 / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus circulans (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsIkegami, T. / Okada, T. / Hashimoto, M. / Seino, S. / Watanabe, T. / Shirakawa, M.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Solution structure of the chitin-binding domain of Bacillus circulans WL-12 chitinase A1.
Authors: Ikegami, T. / Okada, T. / Hashimoto, M. / Seino, S. / Watanabe, T. / Shirakawa, M.
History
DepositionJan 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: CHITINASE A1


Theoretical massNumber of molelcules
Total (without water)5,0391
Polymers5,0391
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)30 / 100structures with the lowest energy
RepresentativeModel #26closest to the average

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Components

#1: Protein/peptide CHITINASE A1 / (CHBD-CHIA1)


Mass: 5038.625 Da / Num. of mol.: 1 / Fragment: CHITIN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: WL-12 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P20533, chitinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D NOESY
1213D 15N-separated NOESY
131HMQC-J
NMR detailsText: This structure was determined using a uniformly 15N-labeled ChBD-ChiA1. Stereospecific assignments of the methyl groups of the leucine and valine residues were achieved with 15% fractionally ...Text: This structure was determined using a uniformly 15N-labeled ChBD-ChiA1. Stereospecific assignments of the methyl groups of the leucine and valine residues were achieved with 15% fractionally 13C-labeled ChBD-ChiA1 dissolved in 99.8% D2O.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0 mM 15N-labeled ChBD-ChiA1 in 10 mM KH2PO4-K2HPO4 (pH 6.0) and 10 mM deuterated dithiothreitol (DTT)90% H2O/10% D2O
21.2 mM 15N-labeled ChBD-ChiA1 in 100 mM KH2PO4-K2HPO4 (pH 6.0) and 10 mM deuterated DTT99.8% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1106ambient 310 K
21006ambient 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerrefinement
DYANA1.5Guentertstructure solution
NMRPipe1.7Delaglioprocessing
XwinNMR2Brukercollection
nmrPipp4.2.4Garrettdata analysis
MOLMOL2.3Koradidata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 493 NOE-based distance, 20 hydrogen bond, and 33 dihedral angle constraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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