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- PDB-5nmy: NMR solution structure of lysostaphin -

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Basic information

Entry
Database: PDB / ID: 5nmy
TitleNMR solution structure of lysostaphin
ComponentsLysostaphin
KeywordsHYDROLASE / peptidoglycan / M23 / peptidase / bacterial SH3
Function / homology
Function and homology information


lysostaphin / cell wall organization / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
: / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 ...: / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / SH3 Domains / Distorted Sandwich / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus simulans (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTossavainen, H. / Raulinaitis, V. / Permi, P.
CitationJournal: Front Mol Biosci / Year: 2018
Title: Structural and Functional Insights Into Lysostaphin-Substrate Interaction.
Authors: Tossavainen, H. / Raulinaitis, V. / Kauppinen, L. / Pentikainen, U. / Maaheimo, H. / Permi, P.
History
DepositionApr 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9412
Polymers26,8761
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint-33 kcal/mol
Surface area13910 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Lysostaphin / Glycyl-glycine endopeptidase


Mass: 26876.070 Da / Num. of mol.: 1 / Fragment: UNP residues 251-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus simulans (bacteria) / Gene: lss / Production host: Escherichia coli (E. coli) / References: UniProt: P10547, lysostaphin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
191isotropic13D H(CCO)NH
181isotropic13D C(CO)NH
171isotropic13D HBHA(CO)NH
161isotropic13D 1H-15N NOESY
1111isotropic12D (HB)CB(CGCD)HD
1101isotropic12D (HB)CB(CGCDCE)HE
2122isotropic13D 1H-13C NOESY aliphatic
2142isotropic13D 1H-13C NOESY aromatic
2132isotropic13D (H)CCH-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.36 mM [U-13C; U-15N] lysostaphin, 20 mM Bis-Tris, 0.36 mM ZnCl2, 93% H2O/7% D2Osample193% H2O/7% D2O
solution20.47 mM [U-13C; U-15N] lysostaphin, 20 mM Bis-Tris, 0.36 mM ZnCl2, 100% D2Osample2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.36 mMlysostaphin[U-13C; U-15N]1
20 mMBis-Trisnatural abundance1
0.36 mMZnCl2natural abundance1
0.47 mMlysostaphin[U-13C; U-15N]2
20 mMBis-Trisnatural abundance2
0.36 mMZnCl2natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.15 Msample16.5ambient atm308 K
20.15 Msample26.5ambient atm308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
VNMRVarianprocessing
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 15

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