#200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (4)
-
Assembly
Deposited unit
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein
x 5
icosahedral pentamer
1.04 MDa, 35 polymers
Theoretical mass
Number of molelcules
Total (without water)
1,040,843
35
Polymers
1,040,843
35
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
point symmetry operation
4
4
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein
x 6
icosahedral 23 hexamer
1.25 MDa, 42 polymers
Theoretical mass
Number of molelcules
Total (without water)
1,249,011
42
Polymers
1,249,011
42
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
point symmetry operation
5
5
Idetical with deposited unit
icosahedral asymmetric unit, std point frame
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
6
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein
x 15
crystal asymmetric unit, crystal frame
3.12 MDa, 105 polymers
Theoretical mass
Number of molelcules
Total (without water)
3,122,528
105
Polymers
3,122,528
105
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
2
point symmetry operation
14
Unit cell
Length a, b, c (Å)
553.033, 574.390, 587.358
Angle α, β, γ (deg.)
90.00, 90.00, 90.00
Int Tables number
23
Space group name H-M
I222
Symmetry
Point symmetry: (Schoenflies symbol: I (icosahedral))
Mass: 29738.361 Da / Num. of mol.: 7 / Mutation: W336F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Gene: 5 / Cell line (production host): BL21-DE3(plys-S) / Production host: Escherichia coli (E. coli) / References: UniProt: P49861
Sequence details
THE FIRST 103 RESIDUES ARE CLEAVED. THE SEQUENCE OF PROHEAD II BEGINS AT RESIDUE 104. THERE IS ...THE FIRST 103 RESIDUES ARE CLEAVED. THE SEQUENCE OF PROHEAD II BEGINS AT RESIDUE 104. THERE IS DYNAMICS IN THE N-TERMINUS REGION THEREFORE SOME N-TERMINAL RESIDUES COULD NOT BE MODELED IN THE CRYSTAL STRUCTURE. THE CONSTRUCT WAS ALSO TRUNCATED BETWEEN RESIDUE 159-171 AND REPLACED BY THE LINKER APGD.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 29
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Sample preparation
Crystal
Density Matthews: 7.48 Å3/Da / Density % sol: 83.6 %
Crystal grow
Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100mM CHES pH 9.0, 200mM Manganese Chloride, 2.7% PEG 4k, 200mM NDSB-211(in drop only), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution: 3.65→3.74 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.4 / Num. unique all: 11086 / Rsym value: 0.431 / % possible all: 14.8
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
SCALA
datascaling
CNS
refinement
PDB_EXTRACT
3.006
dataextraction
DENZO
datareduction
SCALEPACK
datascaling
RAVE
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Prohead II 12A Cryo-EM model and PII 5.2A crystal structure Resolution: 3.65→35 Å / Occupancy max: 1 / Occupancy min: 1 / σ(I): 0 Details: cross validation was not used and R-free was not calculated due to the high NCS symmetry (15-fold).
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