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- PDB-2ls0: Solution Structure of the Target Recognition Domain of Zoocin A -

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Basic information

Entry
Database: PDB / ID: 2ls0
TitleSolution Structure of the Target Recognition Domain of Zoocin A
ComponentsZoocin A endopeptidase
KeywordsHYDROLASE / specificity
Function / homology
Function and homology information


lysostaphin / septum digestion after cytokinesis / : / cell division site / cell outer membrane / metalloendopeptidase activity
Similarity search - Function
Target recognition domain of lytic exoenzyme / Lytic exoenzyme, target recognition domain / Lytic exoenzyme, target recognition domain superfamily / Target recognition domain of lytic exoenzyme / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidase, M23/M37 family
Similarity search - Component
Biological speciesStreptococcus equi subsp. zooepidemicus (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsTimkovich, R. / Chen, Y. / Simmonds, R.S.
CitationJournal: Proteins / Year: 2013
Title: Solution structure of the recombinant target recognition domain of zoocin A.
Authors: Chen, Y. / Simmonds, R.S. / Young, J.K. / Timkovich, R.
History
DepositionApr 17, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Mar 27, 2013Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Zoocin A endopeptidase


Theoretical massNumber of molelcules
Total (without water)14,0901
Polymers14,0901
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Zoocin A endopeptidase


Mass: 14089.651 Da / Num. of mol.: 1 / Fragment: UNP residues 170-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus equi subsp. zooepidemicus (bacteria)
Gene: zooA / Production host: Escherichia coli (E. coli) / References: UniProt: O54308

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1332D 1H-1H TOCSY
1432D DQF-COSY
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HN(CA)CB
1913D HN(CO)CA
11013D (H)CCH-TOCSY
11113D HNHA
11213D 1H-15N NOESY
11323D 1H-15N TOCSY
11413D 1H-13C NOESY
11513D CCC-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.4 mM [U-95% 13C; U-90% 15N] protein, 10 mM potassium phosphate, 0.1 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.7-1.4 mM [U-90% 15N] protein, 10 mM potassium phosphate, 0.1 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.7-1.4 mM protein, 10 mM potassium phosphate, 0.1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
40.7-1.4 mM protein, 10 mM potassium phosphate, 0.1 mM sodium azide, 99.8% D2O99.8% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
2.4 mMentity-1[U-95% 13C; U-90% 15N]1
10 mMpotassium phosphate-21
0.1 mMsodium azide-31
mMentity-4[U-90% 15N]0.7-1.42
10 mMpotassium phosphate-52
0.1 mMsodium azide-62
mMentity-70.7-1.43
10 mMpotassium phosphate-83
0.1 mMsodium azide-93
mMentity-100.7-1.44
10 mMpotassium phosphate-114
0.1 mMsodium azide-124
Sample conditionsIonic strength: 0.02 / pH: 7.0 / Pressure: ambient / Temperature: 297 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
TopSpin1.2Bruker Biospincollection
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
PIPPGarrettpeak picking
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
SparkyGoddarddata analysis
ARIA2Linge, O'Donoghue and Nilgesstructure solution
ProcheckNMRLaskowski and MacArthurquality checking
TALOSCornilescu, Delaglio and Baxdiheral determination
PyMOL1.5.0.1Schrodinger, LLCmolecular graphics
DeepView/Swiss-PDBViewerGuex, Peitsch, Schwede, and Diemandmolecular graphics
RefinementMethod: simulated annealing, molecular dynamics / 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: 10

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