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- PDB-1k0h: Solution structure of bacteriophage lambda gpFII -

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Basic information

Entry
Database: PDB / ID: 1k0h
TitleSolution structure of bacteriophage lambda gpFII
ComponentsgpFII
KeywordsVIRAL PROTEIN / twisted beta-sandwich
Function / homology
Function and homology information


virion assembly / virion component / host cell cytoplasm
Similarity search - Function
Phage tail proteins / Bacteriophage tail attachment protein FII / : / Phage Head-Tail Attachment protein / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Head-tail connector protein FII
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsMaxwell, K.L. / Yee, A.A. / Arrowsmith, C.H. / Gold, M. / Davidson, A.R.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The solution structure of the bacteriophage lambda head-tail joining protein, gpFII.
Authors: Maxwell, K.L. / Yee, A.A. / Arrowsmith, C.H. / Gold, M. / Davidson, A.R.
History
DepositionSep 19, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gpFII


Theoretical massNumber of molelcules
Total (without water)12,7751
Polymers12,7751
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)10 / 50structures with the lowest energy
RepresentativeModel #2lowest energy

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Components

#1: Protein gpFII / Tail attachment protein


Mass: 12775.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: FII / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(LAMBDADE3) / References: UniProt: P03714

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.3mM gpFII U-15N, 13C; 10MM PHOSPHATE BUFFER NA, 200MM NACL
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 200mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerrefinement
NMRPipe1.7Frank Delaglioprocessing
XEASY1.3.1Tai-he Xia and Christian Bartelsdata analysis
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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