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- PDB-2lhs: Structure of the chitin binding protein 21 (CBP21) -

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Basic information

Entry
Database: PDB / ID: 2lhs
TitleStructure of the chitin binding protein 21 (CBP21)
ComponentsCBP21
KeywordsChitin Binding Protein
Function / homology
Function and homology information


chitin catabolic process
Similarity search - Function
chitin-binding protein cbp21 / : / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
Chitin-binding protein
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 20
AuthorsAachmann, F.L. / Eijsink, V.G. / Vaaje-Kolstad, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: NMR structure of a lytic polysaccharide monooxygenase provides insight into copper binding, protein dynamics, and substrate interactions.
Authors: Aachmann, F.L. / Sorlie, M. / Skjak-Braek, G. / Eijsink, V.G. / Vaaje-Kolstad, G.
History
DepositionAug 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Aug 13, 2014Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_sheet.number_strands
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI
Remark 650 HELIX DETERMINATION METHOD: AUTHOR
Remark 700 SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBP21


Theoretical massNumber of molelcules
Total (without water)18,8131
Polymers18,8131
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)20 / 256target function
RepresentativeModel #1fewest violations

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Components

#1: Protein CBP21 / Chitin-binding protein


Mass: 18812.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: BJL200 / Gene: cbp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83009
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-13C NOESY aliphatic
1213D 1H-15N NOESY
1332D 1H-1H TOCSY
1432D DQF-COSY
1532D 1H-1H NOESY
1622D 1H-13C HSQC aromatic
1742D DQF-COSY
1842D 1H-1H TOCSY
1942D 1H-1H NOESY
11012D 1H-13C HSQC aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.2 mM [U-98% 13C; U-98% 15N] CBP21, 20 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.8-1.2 mM [U-98% 13C; U-98% 15N] CBP21, 20 mM potassium phosphate, 10 mM sodium chloride, 100% D2O100% D2O
30.8-1.2 mM CBP21, 20 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
40.8-1.2 mM CBP21, 20 mM potassium phosphate, 10 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCBP21-1[U-98% 13C; U-98% 15N]0.8-1.21
20 mMpotassium phosphate-21
10 mMsodium chloride-31
mMCBP21-4[U-98% 13C; U-98% 15N]0.8-1.22
20 mMpotassium phosphate-52
10 mMsodium chloride-62
mMCBP21-70.8-1.23
20 mMpotassium phosphate-83
10 mMsodium chloride-93
mMCBP21-100.8-1.24
20 mMpotassium phosphate-114
10 mMsodium chloride-124
Sample conditionsIonic strength: 0.06 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels et al.collection
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
YASARAKrieger, Darden, Nabuurs, Finkelstein, Vriendrefinement
CYANAKrieger, Darden, Nabuurs, Finkelstein, Vriendrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 256 / Conformers submitted total number: 20

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