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- PDB-7tjm: Bacteriophage Q beta capsid protein in T3 symmetry -

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Basic information

Entry
Database: PDB / ID: 7tjm
TitleBacteriophage Q beta capsid protein in T3 symmetry
ComponentsMinor capsid protein A1
KeywordsVIRUS LIKE PARTICLE / bacteriophage Q beta capsid / T3 symmetry
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Read-through domain / Read-through domain / MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Minor capsid protein A1
Similarity search - Component
Biological speciesBacteriophage sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å
AuthorsJin, X.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
Citation
Journal: To Be Published
Title: Alternative Assembly of Q beta Virus-like Particles
Authors: Shaw, V. / Sungsuwan, S. / McFall-Boegeman, H. / Huang, X. / Jin, X.
#1: Journal: ACS Chemical Biology / Year: 2022
Title: Structure Guided Design of Bacteriophage Q beta Mutants as Next Generation Carriers for Conjugate Vaccines
Authors: Sungsuwan, S. / Wu, X. / Shaw, V. / McFall-Boegeman, H. / Rashidijahanabad, Z. / Tan, Z. / Lang, S. / Tahmasebi Nick, S. / Lin, P. / Yin, Z. / Ramadan, S. / Jin, X. / Huang, X.
History
DepositionJan 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Minor capsid protein A1
a: Minor capsid protein A1
B: Minor capsid protein A1
b: Minor capsid protein A1
C: Minor capsid protein A1
c: Minor capsid protein A1
D: Minor capsid protein A1
d: Minor capsid protein A1
E: Minor capsid protein A1
e: Minor capsid protein A1
1: Minor capsid protein A1
U: Minor capsid protein A1
F: Minor capsid protein A1
f: Minor capsid protein A1
G: Minor capsid protein A1
g: Minor capsid protein A1
H: Minor capsid protein A1
h: Minor capsid protein A1
I: Minor capsid protein A1
i: Minor capsid protein A1
J: Minor capsid protein A1
j: Minor capsid protein A1
5: Minor capsid protein A1
Y: Minor capsid protein A1
K: Minor capsid protein A1
k: Minor capsid protein A1
L: Minor capsid protein A1
l: Minor capsid protein A1
M: Minor capsid protein A1
m: Minor capsid protein A1
N: Minor capsid protein A1
n: Minor capsid protein A1
O: Minor capsid protein A1
o: Minor capsid protein A1
9: Minor capsid protein A1
v: Minor capsid protein A1
P: Minor capsid protein A1
p: Minor capsid protein A1
Q: Minor capsid protein A1
q: Minor capsid protein A1
R: Minor capsid protein A1
r: Minor capsid protein A1
S: Minor capsid protein A1
s: Minor capsid protein A1
T: Minor capsid protein A1
t: Minor capsid protein A1
w: Minor capsid protein A1
x: Minor capsid protein A1
2: Minor capsid protein A1
V: Minor capsid protein A1
3: Minor capsid protein A1
W: Minor capsid protein A1
4: Minor capsid protein A1
X: Minor capsid protein A1
6: Minor capsid protein A1
Z: Minor capsid protein A1
7: Minor capsid protein A1
u: Minor capsid protein A1
8: Minor capsid protein A1
0: Minor capsid protein A1


Theoretical massNumber of molelcules
Total (without water)848,21260
Polymers848,21260
Non-polymers00
Water00
1
A: Minor capsid protein A1
a: Minor capsid protein A1
B: Minor capsid protein A1
b: Minor capsid protein A1
C: Minor capsid protein A1
c: Minor capsid protein A1
D: Minor capsid protein A1
d: Minor capsid protein A1
E: Minor capsid protein A1
e: Minor capsid protein A1
1: Minor capsid protein A1
U: Minor capsid protein A1
F: Minor capsid protein A1
f: Minor capsid protein A1
G: Minor capsid protein A1
g: Minor capsid protein A1
H: Minor capsid protein A1
h: Minor capsid protein A1
I: Minor capsid protein A1
i: Minor capsid protein A1
J: Minor capsid protein A1
j: Minor capsid protein A1
5: Minor capsid protein A1
Y: Minor capsid protein A1
K: Minor capsid protein A1
k: Minor capsid protein A1
L: Minor capsid protein A1
l: Minor capsid protein A1
M: Minor capsid protein A1
m: Minor capsid protein A1
N: Minor capsid protein A1
n: Minor capsid protein A1
O: Minor capsid protein A1
o: Minor capsid protein A1
9: Minor capsid protein A1
v: Minor capsid protein A1
P: Minor capsid protein A1
p: Minor capsid protein A1
Q: Minor capsid protein A1
q: Minor capsid protein A1
R: Minor capsid protein A1
r: Minor capsid protein A1
S: Minor capsid protein A1
s: Minor capsid protein A1
T: Minor capsid protein A1
t: Minor capsid protein A1
w: Minor capsid protein A1
x: Minor capsid protein A1
2: Minor capsid protein A1
V: Minor capsid protein A1
3: Minor capsid protein A1
W: Minor capsid protein A1
4: Minor capsid protein A1
X: Minor capsid protein A1
6: Minor capsid protein A1
Z: Minor capsid protein A1
7: Minor capsid protein A1
u: Minor capsid protein A1
8: Minor capsid protein A1
0: Minor capsid protein A1

A: Minor capsid protein A1
a: Minor capsid protein A1
B: Minor capsid protein A1
b: Minor capsid protein A1
C: Minor capsid protein A1
c: Minor capsid protein A1
D: Minor capsid protein A1
d: Minor capsid protein A1
E: Minor capsid protein A1
e: Minor capsid protein A1
1: Minor capsid protein A1
U: Minor capsid protein A1
F: Minor capsid protein A1
f: Minor capsid protein A1
G: Minor capsid protein A1
g: Minor capsid protein A1
H: Minor capsid protein A1
h: Minor capsid protein A1
I: Minor capsid protein A1
i: Minor capsid protein A1
J: Minor capsid protein A1
j: Minor capsid protein A1
5: Minor capsid protein A1
Y: Minor capsid protein A1
K: Minor capsid protein A1
k: Minor capsid protein A1
L: Minor capsid protein A1
l: Minor capsid protein A1
M: Minor capsid protein A1
m: Minor capsid protein A1
N: Minor capsid protein A1
n: Minor capsid protein A1
O: Minor capsid protein A1
o: Minor capsid protein A1
9: Minor capsid protein A1
v: Minor capsid protein A1
P: Minor capsid protein A1
p: Minor capsid protein A1
Q: Minor capsid protein A1
q: Minor capsid protein A1
R: Minor capsid protein A1
r: Minor capsid protein A1
S: Minor capsid protein A1
s: Minor capsid protein A1
T: Minor capsid protein A1
t: Minor capsid protein A1
w: Minor capsid protein A1
x: Minor capsid protein A1
2: Minor capsid protein A1
V: Minor capsid protein A1
3: Minor capsid protein A1
W: Minor capsid protein A1
4: Minor capsid protein A1
X: Minor capsid protein A1
6: Minor capsid protein A1
Z: Minor capsid protein A1
7: Minor capsid protein A1
u: Minor capsid protein A1
8: Minor capsid protein A1
0: Minor capsid protein A1

A: Minor capsid protein A1
a: Minor capsid protein A1
B: Minor capsid protein A1
b: Minor capsid protein A1
C: Minor capsid protein A1
c: Minor capsid protein A1
D: Minor capsid protein A1
d: Minor capsid protein A1
E: Minor capsid protein A1
e: Minor capsid protein A1
1: Minor capsid protein A1
U: Minor capsid protein A1
F: Minor capsid protein A1
f: Minor capsid protein A1
G: Minor capsid protein A1
g: Minor capsid protein A1
H: Minor capsid protein A1
h: Minor capsid protein A1
I: Minor capsid protein A1
i: Minor capsid protein A1
J: Minor capsid protein A1
j: Minor capsid protein A1
5: Minor capsid protein A1
Y: Minor capsid protein A1
K: Minor capsid protein A1
k: Minor capsid protein A1
L: Minor capsid protein A1
l: Minor capsid protein A1
M: Minor capsid protein A1
m: Minor capsid protein A1
N: Minor capsid protein A1
n: Minor capsid protein A1
O: Minor capsid protein A1
o: Minor capsid protein A1
9: Minor capsid protein A1
v: Minor capsid protein A1
P: Minor capsid protein A1
p: Minor capsid protein A1
Q: Minor capsid protein A1
q: Minor capsid protein A1
R: Minor capsid protein A1
r: Minor capsid protein A1
S: Minor capsid protein A1
s: Minor capsid protein A1
T: Minor capsid protein A1
t: Minor capsid protein A1
w: Minor capsid protein A1
x: Minor capsid protein A1
2: Minor capsid protein A1
V: Minor capsid protein A1
3: Minor capsid protein A1
W: Minor capsid protein A1
4: Minor capsid protein A1
X: Minor capsid protein A1
6: Minor capsid protein A1
Z: Minor capsid protein A1
7: Minor capsid protein A1
u: Minor capsid protein A1
8: Minor capsid protein A1
0: Minor capsid protein A1


Theoretical massNumber of molelcules
Total (without water)2,544,637180
Polymers2,544,637180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area976300 Å2
ΔGint-5953 kcal/mol
Surface area906080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)286.627, 286.627, 662.678
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ...
Minor capsid protein A1 / A1 read-through protein


Mass: 14136.874 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE1
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.18 Å3/Da / Density % sol: 80.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: PEG 3350, cobalt chloride, Tris / PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.54→49.56 Å / Num. obs: 247697 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.8 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.4
Reflection shellResolution: 3.54→3.62 Å / Num. unique obs: 17430 / CC1/2: 0.15

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qbe

1qbe


Resolution: 3.54→49.56 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.852 / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.604 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3278 12266 5 %RANDOM
Rwork0.2782 ---
obs0.2806 234901 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 208.92 Å2 / Biso mean: 131.48 Å2 / Biso min: 56.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å20 Å2
2---0.3 Å20 Å2
3---0.96 Å2
Refinement stepCycle: final / Resolution: 3.54→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59580 0 0 0 59580
Num. residues----7920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01362302
X-RAY DIFFRACTIONr_bond_other_d0.0030.01560614
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.65784960
X-RAY DIFFRACTIONr_angle_other_deg1.1511.581139226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.31158100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82122.8823026
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.7461510256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.89315430
X-RAY DIFFRACTIONr_chiral_restr0.0750.28726
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0272156
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0213776
LS refinement shellResolution: 3.54→3.632 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 901 -
Rwork0.469 17430 -
all-18331 -
obs--99.99 %

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