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- PDB-2lfp: Structure of bacteriophage SPP1 gp17 protein -

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Basic information

Entry
Database: PDB / ID: 2lfp
TitleStructure of bacteriophage SPP1 gp17 protein
ComponentsBacteriophage SPP1 complete nucleotide sequence
KeywordsVIRAL PROTEIN
Function / homologySTM4215-like - #30 / STM4215-like / Tail completion protein / Protein of unknown function (DUF3168) / virus tail fiber assembly / virus tail / 2-Layer Sandwich / Alpha Beta / Tail completion protein gp17
Function and homology information
Biological speciesBacillus phage SPP1 (virus)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChagot, B. / Auzat, I. / Gallopin, M. / Petitpas, I. / Gilquin, B. / Tavares, P. / Zinn-Justin, S.
CitationJournal: Proteins / Year: 2012
Title: Solution structure of gp17 from the Siphoviridae bacteriophage SPP1: Insights into its role in virion assembly.
Authors: Chagot, B. / Auzat, I. / Gallopin, M. / Petitpas, I. / Gilquin, B. / Tavares, P. / Zinn-Justin, S.
History
DepositionJul 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophage SPP1 complete nucleotide sequence


Theoretical massNumber of molelcules
Total (without water)15,4781
Polymers15,4781
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)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bacteriophage SPP1 complete nucleotide sequence


Mass: 15478.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPP1 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: O48448

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D HN(CO)CA
1913D (H)CCH-COSY
11013D HN(CA)CO
11113D HBHA(CO)NH
11222D 1H-1H TOCSY
11322D 1H-1H COSY
11422D 1H-1H NOESY
2153T1 relaxation
2163T2 relaxation
2173heteronuclear NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM protein, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMprotein-1[U-100% 13C; U-100% 15N]1
0.3 mMprotein-22
0.6 mMprotein-3[U-100% 13C; U-100% 15N]3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.05 7.5 ambient 298 K
20.5 6.0 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX7001
Bruker AMXBrukerAMX6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
Sparky1.3Goddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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