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- PDB-1x60: Solution structure of the peptidoglycan binding domain of B. subt... -

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Basic information

Entry
Database: PDB / ID: 1x60
TitleSolution structure of the peptidoglycan binding domain of B. subtilis cell wall lytic enzyme CwlC
ComponentsSporulation-specific N-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / CwlC / CwlCr / peptidoglycan / cell wall lytic amidase / tandem repeats
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / outer membrane-bounded periplasmic space / extracellular region / metal ion binding
Similarity search - Function
Sporulation related repeat / Sporulation-like domain / Sporulation-like domain superfamily / SPOR domain / SPOR domain profile. / : / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Alpha-Beta Plaits ...Sporulation related repeat / Sporulation-like domain / Sporulation-like domain superfamily / SPOR domain / SPOR domain profile. / : / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sporulation-specific N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMishima, M. / Shida, T. / Yabuki, K. / Kato, K. / Sekiguchi, J. / Kojima, C.
CitationJournal: Biochemistry / Year: 2005
Title: Solution Structure of the Peptidoglycan Binding Domain of Bacillus subtilis Cell Wall Lytic Enzyme CwlC: Characterization of the Sporulation-Related Repeats by NMR(,)
Authors: Mishima, M. / Shida, T. / Yabuki, K. / Kato, K. / Sekiguchi, J. / Kojima, C.
History
DepositionMay 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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: Sporulation-specific N-acetylmuramoyl-L-alanine amidase


Theoretical massNumber of molelcules
Total (without water)8,2621
Polymers8,2621
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 #1lowest energy

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Components

#1: Protein Sporulation-specific N-acetylmuramoyl-L-alanine amidase / Cell wall hydrolase / Autolysin


Mass: 8262.405 Da / Num. of mol.: 1 / Fragment: residues 1-79
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pQE30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q06320, N-acetylmuramoyl-L-alanine amidase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.7mM CwlCr U-15N,13C 50mM phosphate buffer K; 100% D2O100% D2O
21.7mM CwlCr U-15N 50mM phosphate buffer K; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 70mM / pH: 6.9 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, F.processing
Sparky3.11Goddard, T.D.data analysis
CYANA1.05Herrmann, T.structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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