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- PDB-7qjf: Llp mutant C1G, lytic conversion lipoprotein of phage T5 -

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Basic information

Entry
Database: PDB / ID: 7qjf
TitleLlp mutant C1G, lytic conversion lipoprotein of phage T5
ComponentsLytic conversion lipoprotein
KeywordsVIRAL PROTEIN / Phage protein / Periplasmic protein / Soluble of acylated WT protein STRUCTURE FROM UNIO / UNIO VERSION 2.9.5
Function / homologynegative regulation of receptor-mediated virion attachment to host cell / superinfection exclusion / host cell plasma membrane / membrane / Lytic conversion lipoprotein
Function and homology information
Biological speciesEscherichia phage T5 (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsDegroux, S. / Mestdach, E. / Vives, C. / Le Roy, A. / Salmon, L. / Herrman, T. / Breyton, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0023 France
CitationJournal: To Be Published
Title: Llp mutant C1G, lytic conversion lipoprotein of phage T5
Authors: Degroux, S. / Mestdach, E. / Vives, C. / Le Roy, A. / Salmon, L. / Herrman, T. / Breyton, C.
History
DepositionDec 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lytic conversion lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,0531
Polymers7,0531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lytic conversion lipoprotein


Mass: 7052.991 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Mutated version of the lytic conversion lipoprotein produced from a MBP-Llp fusion protein with TEV cleavage site. The mature protein results in the same protein sequence as the WT protein, ...Details: Mutated version of the lytic conversion lipoprotein produced from a MBP-Llp fusion protein with TEV cleavage site. The mature protein results in the same protein sequence as the WT protein, with a Glycine in amino acide +1 in place of the acylated cysteine.
Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: llp, T5.158, T5p154 / Plasmid: pMAL-p2E / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q38162
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY aliphatic
1121isotropic23D 1H-13C NOESY aromatic
1131isotropic23D 1H-15N-13C NOESY
121isotropic23D 1H-13C TOCSY
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HNCA
161isotropic13D HN(CO)CA
171isotropic13D HN(CA)CB
181isotropic13D HN(COCA)CB
191isotropic1HAHBNH
1101isotropic1HAHB(CO)NH
1111isotropic12D 15N-HSQC

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Sample preparation

DetailsType: solution
Contents: 25 mM no Tris, 75 mM no NaCl, 1.024 mM 13C 15N Sol-Llp, 90% H2O/10% D2O
Details: Sol-Llp protein is soluble and the buffer is 25 mM Tris pH6.5, 75 mM NaCL.
Label: 15N_C13_Sol-Llp / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMTrisno1
75 mMNaClno1
1.024 mMSol-Llp13C 15N1
Sample conditionsIonic strength: 75 mM / Label: 15N_C13_Sol-Llp / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE10002

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Processing

NMR software
NameVersionDeveloperClassification
UNIO2.9.5Torsten Herrmannchemical shift assignment
UNIO2.9.5Torsten Herrmanndata analysis
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.3Brungerrefinement
CcpNmr AnalysisCCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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