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- PDB-2lsm: Solution structure of gpFI C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2lsm
TitleSolution structure of gpFI C-terminal domain
ComponentsDNA-packaging protein FI
KeywordsCHAPERONE / gene product FI / phage lambda / DNA packaging
Function / homology
Function and homology information


viral genome packaging / host cell cytoplasm
Similarity search - Function
DNA packaging chaperone protein FI, C-terminal beta-strand domain / DNA packaging protein FI / DNA packaging protein FI, C-terminal beta-strand domain / DNA packaging protein FI / Ribosomal Protein L9; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-packaging protein FI
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsPopovic, A. / Wu, B. / Edwards, A.M. / Davidson, A.R. / Maxwell, K.L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and biochemical characterization of phage lambda FI protein (gpFI) reveals a novel mechanism of DNA packaging chaperone activity.
Authors: Popovic, A. / Wu, B. / Arrowsmith, C.H. / Edwards, A.M. / Davidson, A.R. / Maxwell, K.L.
History
DepositionMay 2, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
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: DNA-packaging protein FI


Theoretical massNumber of molelcules
Total (without water)6,4951
Polymers6,4951
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-packaging protein FI


Mass: 6495.458 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: FI / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P03709

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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 H(CCO)NH
1313D HNCO
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D 1H-15N NOESY
1723D 1H-13C NOESY
1813D C(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] polypeptide, 25 mM sodium phosphate, 250 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] polypeptide, 25 mM sodium phosphate, 250 mM potassium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMpolypeptide-1[U-99% 13C; U-99% 15N]1
25 mMsodium phosphate-21
250 mMsodium chloride-31
1 mMpolypeptide-4[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-52
250 mMpotassium chloride-62
Sample conditionsIonic strength: 250 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA_2.0Guntert, Mumenthaler and Wuthrichrefinement
CYANA_2.0Guntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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