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- PDB-4uw7: Structure of the carboxy-terminal domain of the bacteriophage T5 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uw7 | ||||||
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Title | Structure of the carboxy-terminal domain of the bacteriophage T5 L- shaped tail fiber without its intra-molecular chaperone domain | ||||||
![]() | L-SHAPED TAIL FIBER PROTEIN | ||||||
![]() | VIRAL PROTEIN / BACTERIAL VIRUSES / CAUDOVIRALES / SIPHOVIRIDAE / INFECTION. | ||||||
Function / homology | ![]() lipopolysaccharide-mediated virion attachment to host cell / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / symbiont entry into host cell / proteolysis Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garcia-Doval, C. / Luque, D. / Caston, J.R. / Otero, J.M. / Llamas-Saiz, A.L. / Boulanger, P. / van Raaij, M.J. | ||||||
![]() | ![]() Title: Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone. Authors: Garcia-Doval, C. / Caston, J.R. / Luque, D. / Granell, M. / Otero, J.M. / Llamas-Saiz, A.L. / Renouard, M. / Boulanger, P. / van Raaij, M.J. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Crystallization of the C-Terminal Domain of the Bacteriophage T5 L-Shaped Fibre. Authors: Garcia-Doval, C. / Luque, D. / Caston, J.R. / Boulanger, P. / van Raaij, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.8 KB | Display | ![]() |
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PDB format | ![]() | 135.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 31078.691 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN, RESIDUES 970-1263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 0.1 M TRIS-HCL PH 8.5, 17.5% (W/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013 / Details: HORIZONTAL AND VERTICAL FOCUSSING MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→56.2 Å / Num. obs: 30585 / % possible obs: 96.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.52→2.59 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.52→56.19 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.622 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.75 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.062 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→56.19 Å
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Refine LS restraints |
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