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- PDB-9eum: NMR structure of the Staphylococcus aureus bacteriophage phi812 h... -

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Basic information

Entry
Database: PDB / ID: 9eum
TitleNMR structure of the Staphylococcus aureus bacteriophage phi812 hub protein - lytic cleaver (CHAP) domain
ComponentsPeptidase C51 domain-containing protein
KeywordsHYDROLASE / CHAP / phi812 / peptidase / peptidoglycan
Function / homologysymbiont-mediated cytolysis of host cell / CHAP domain profile. / CHAP domain / CHAP domain / Papain-like cysteine peptidase superfamily / Peptidase C51 domain-containing protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsBinovsky, J. / Tripsianes, K. / Novacek, J. / Benesik, M. / Plevka, P.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103
CitationJournal: To Be Published
Title: Cell attachment and tail contraction of S. aureus phage phi812
Authors: Binovsky, J. / Tripsianes, K. / Novacek, J. / Benesik, M. / Plevka, P.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase C51 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)18,9271
Polymers18,9271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidase C51 domain-containing protein


Mass: 18927.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 812 (virus) / Gene: 812_113, 812a_113, 812F1_113, K1/420_113, K1_113 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U1X189
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic14D HC(CC TOCSY(CO))NH
121isotropic14D 13C,15N edited HMQC-NOESY-HSQC
131isotropic14D 13C,13C edited HMQC-NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 1.8 mM [U-99% 13C; U-99% 15N] CHAP domain, 90% H2O/10% D2O
Label: 13C_15N_CHAP / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.8 mM / Component: CHAP domain / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 100 mM / Label: NMR / pH: 6.6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
4D-CHAINSEvangelidis and Tripsianeschemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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