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- PDB-5kqc: Identification and structural characterization of LytU -

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Basic information

Entry
Database: PDB / ID: 5kqc
TitleIdentification and structural characterization of LytU
ComponentsPeptidase M23
KeywordsHYDROLASE / lysostaphin / LytU / peptidoglycan / zinc
Function / homology
Function and homology information


lysostaphin / membrane => GO:0016020 / metalloendopeptidase activity / metallopeptidase activity / membrane
Similarity search - Function
Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Lysostaphin / lysostaphin
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTossavainen, H. / Raulinaitis, V. / Permi, P.
CitationJournal: Sci Rep / Year: 2017
Title: Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family.
Authors: Raulinaitis, V. / Tossavainen, H. / Aitio, O. / Juuti, J.T. / Hiramatsu, K. / Kontinen, V. / Permi, P.
History
DepositionJul 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 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

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Assembly

Deposited unit
A: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3382
Polymers16,2721
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint-36 kcal/mol
Surface area8730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidase M23 / Peptidase family M23


Mass: 16272.134 Da / Num. of mol.: 1 / Fragment: UNP residues 49-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: lytM_3, AS858_11005, ERS093009_01996 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6GI13, UniProt: Q2G1F1*PLUS, 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 HN(COCA)CB
191isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
171isotropic13D (H)CCH-COSY
161isotropic12D (HB)CB(CGCD)HD
1101isotropic12D (HB)CB(CGCDCE)HE
1121isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 1.25 mM zinc chloride, 93% H2O/7% D2O
Label: sample_1 / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLytU[U-13C; U-15N]1
20 mMbisTris buffer1
1.25 mMzinc chloride1
Sample conditionsIonic strength units: Not defined / Label: conditions_1 / pH: 6.5 / Pressure: ambient atm / Temperature: 308 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
VnmrJVariancollection
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 15

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