- PDB-1z1z: NMR structure of the gpu tail protein from lambda bacteriophage -
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Basic information
Entry
Database: PDB / ID: 1z1z
Title
NMR structure of the gpu tail protein from lambda bacteriophage
Components
Minor tail protein U
Keywords
VIRAL 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
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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 13C-separated NOESY
1
2
1
3D 15N-separated NOESY
1
3
1
3D 13C-separated-aromatic NOESY
1
4
1
2D-IPAP-15N HSQC
NMR details
Text: This structure was determined using standard 3D heteronuclear techniques
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Sample preparation
Details
Contents: 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 conditions
Ionic strength: 50 mM KCl / pH: 7.8 / Pressure: 1 atm / Temperature: 293 K
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE
Bruker
AVANCE
600
1
Varian INOVA
Varian
INOVA
800
2
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Processing
NMR software
Name
Version
Developer
Classification
NMRPipe
Delaglio
processing
NMRView
5.2
Johnson
dataanalysis
CYANA
2.1.3
Guntert
structuresolution
XPLOR-NIH
2.9.9
refinement
Refinement
Method: 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 representative
Selection criteria: lowest energy
NMR ensemble
Conformers submitted total number: 1
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