- PDB-2vbe: Tailspike protein of bacteriophage Sf6 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2vbe
Title
Tailspike protein of bacteriophage Sf6
Components
TAILSPIKE-PROTEIN
Keywords
VIRAL PROTEIN / VIRAL ADHESION PROTEIN / TAILSPIKE / OLIGOMERIC RIGHT-HANDED PARALLEL BETA-HELIX
Function / homology
Function and homology information
endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metabolic process / virion attachment to host cell Similarity search - Function
SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.
Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
PROTEIN LACKS N-TERMINAL MET AND HAS 622 AA.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.53 Å3/Da / Density % sol: 51.03 % / Description: NONE
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: VAPOR DIFFUSION HANGING DROP 20 DEG CELSIUS DROP: 3 UL RESERVOIR SNF 3 UL PROTEIN RESERVOIR: 0.1 M MES PH 6.5, 25% PEG 8000, 20 MM MNCL2 PROTEIN: 5MG/ML IN 10 MM SODIUM PHOSPHATE PH 7 ...Details: VAPOR DIFFUSION HANGING DROP 20 DEG CELSIUS DROP: 3 UL RESERVOIR SNF 3 UL PROTEIN RESERVOIR: 0.1 M MES PH 6.5, 25% PEG 8000, 20 MM MNCL2 PROTEIN: 5MG/ML IN 10 MM SODIUM PHOSPHATE PH 7 CRYOCONDITION: 0.1 M MES PH 6.5, 25 % PEG 8000, 20 MM MNCL2
Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9795 Å / Relative weight: 1
Reflection
Resolution: 1.98→19.5 Å / Num. obs: 39829 / % possible obs: 95.6 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.1
Reflection shell
Resolution: 1.98→2.06 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 8 / % possible all: 65.4
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Processing
Software
Name
Version
Classification
REFMAC
5.1.24
refinement
XDS
datareduction
XDS
datascaling
SOLVE
RESOLVE
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 1.98→19.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.104 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.149
2101
5 %
RANDOM
Rwork
0.117
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obs
0.119
39829
95.7 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK