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- PDB-1z1z: NMR structure of the gpu tail protein from lambda bacteriophage -

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Basic information

Entry
Database: PDB / ID: 1z1z
TitleNMR structure of the gpu tail protein from lambda bacteriophage
ComponentsMinor tail protein U
KeywordsVIRAL PROTEIN / mixed alpha-beta / tail protein / bacteriophage
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / host cell cytoplasm
Similarity search - Function
Phage minor tail protein U / Minor tail protein U-like / GpU-like superfamily / Phage minor tail protein U / Phage tail protein-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tail tube terminator protein
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsEdmonds, L. / Maxwell, K. / Davidson, A. / Donaldson, L.W.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The NMR structure of the gpU tail-terminator protein from bacteriophage lambda: identification of sites contributing to Mg(II)-mediated oligomerization and biological function.
Authors: Edmonds, L. / Liu, A. / Kwan, J.J. / Avanessy, A. / Caracoglia, M. / Yang, I. / Maxwell, K.L. / Rubenstein, J. / Davidson, A.R. / Donaldson, L.W.
#1: Journal: To be Published
Title: NMR assignment of the gpu tail protein from lambda bacteriophage
Authors: Edmonds, L. / Thirumoorthy, R.T. / Liu, A. / Davidson, A. / Donaldson, L.W.
History
DepositionMar 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 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: Minor tail protein U


Theoretical massNumber of molelcules
Total (without water)14,6591
Polymers14,6591
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)1 / -
RepresentativeModel #1lowest energy

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Components

#1: Protein Minor tail protein U


Mass: 14659.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses
Description: The full gpu gene was inserted into the NdeI and BamHI sites of pET15b resulting in an amino terminally hexahistidine tagged fusion protein with an intervening thrombin protease cleavage site
Gene: gpu / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03732

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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
1313D 13C-separated-aromatic NOESY
1412D-IPAP-15N HSQC
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques

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Sample preparation

DetailsContents: 0.9 mM gpU, U-15N,13C, 10 mM Tris-d11, pH 7.8, 50 mM potassium chloride, 0.02% sodium azide, 10% D2O, 90% H2O
Solvent system: 10% D2O, 90% H2O
Sample conditionsIonic strength: 50 mM KCl / pH: 7.8 / Pressure: 1 atm / Temperature: 293 K

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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
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglioprocessing
NMRView5.2Johnsondata analysis
CYANA2.1.3Guntertstructure solution
XPLOR-NIH2.9.9refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1180 NOE distance restraints (876 intramolecular, 505 short-range, 128 medium range, 371 long-range), 42 pairs of hydrogen bond distance restraints, 106 pairs of phi/psi dihedral angle ...Details: 1180 NOE distance restraints (876 intramolecular, 505 short-range, 128 medium range, 371 long-range), 42 pairs of hydrogen bond distance restraints, 106 pairs of phi/psi dihedral angle restraints and 41 amide residual dipolar coupling restraints were incorporated into the structure calculation. NOE calibration was performed with CANDID module of CYANA. Initially, 200 structures were calcuated with XPLOR-NIH. From this ensemble, 50 low-energy structure were refined in water using the XPLOR-NIH protocol by C. Spronk. The top 20 structures by energy had a backbone RMSD of 0.96 +/- 0.16 A on the secondary structure elements. In addition to residues 1-3 and 128-131 at the termini, a large loop spanning residues 45-60 is disordered.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers submitted total number: 1

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