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- PDB-1pxq: Structure of Subtilisin A -

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Basic information

Entry
Database: PDB / ID: 1pxq
TitleStructure of Subtilisin A
ComponentsSubtilisin A
KeywordsANTIMICROBIAL PROTEIN / thioether bridge / cyclic peptide / bacteriocin
Function / homologyBacteriocin subtilosin A / Bacteriocin subtilosin A / killing of cells of another organism / defense response to bacterium / extracellular region / Subtilosin-A
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / dynamic annealing
AuthorsKawulka, K.E. / Sprules, T. / McKay, R.T. / Mercier, P. / Diaper, C.M. / Zuber, P. / Vederas, J.C.
Citation
Journal: Biochemistry / Year: 2004
Title: Structure of subtilisin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to alpha-carbon cross-links: formation and reduction of alpha-thio-alpha-amino acid derivatives
Authors: Kawulka, K.E. / Sprules, T. / Diaper, C.M. / Whittal, R.M. / McKay, R.T. / Mercier, P. / Zuber, P. / Vederas, J.C.
#1: Journal: J.Am.Chem.Soc. / Year: 2003
Title: Structure of subtilisin A, an antimicrobial peptide from Bacillus subtilis with unusual posttranslational modifications linking cysteine sulfurs to alpha-carbons of phenylalanine and threonine
Authors: Kawulka, K. / Sprules, T. / McKay, R.T. / Mercier, P. / Diaper, C.M. / Zuber, P. / Vederas, J.C.
History
DepositionJul 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subtilisin A


Theoretical massNumber of molelcules
Total (without water)3,4271
Polymers3,4271
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)8 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Subtilisin A / Antilisterial bacteriocin subtilisin


Mass: 3426.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / Strain: JH642 / References: UniProt: O07623
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1314D 13C/15N-separated NOESY
141HNHA

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Sample preparation

DetailsContents: SubA
Sample conditionsTemperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRcollection
NMRPipe2.2Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.J.'processing
NMRView5Johnson, B.A., Blevins, R.A.J.data analysis
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.structure solution
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.refinement
RefinementMethod: dynamic annealing / Software ordinal: 1
Details: 301 NOE-derived distance constraints and 20 dihedral angle restraints were used to calculate the structures.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 8

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