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- PDB-7tjd: Bacteriophage Q beta capsid protein in T1 symmetry -

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Basic information

Entry
Database: PDB / ID: 7tjd
TitleBacteriophage Q beta capsid protein in T1 symmetry
ComponentsMinor capsid protein A1
KeywordsVIRUS LIKE PARTICLE / bacteriophage Q beta capsid / T1 symmetry
Function / homologyRead-through domain / Read-through domain / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / viral capsid / structural molecule activity / Minor capsid protein A1
Function and homology information
Biological speciesEscherichia virus Qbeta
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsJin, X.
Funding support1items
OrganizationGrant numberCountry
Other private
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Minor capsid protein A1
B: Minor capsid protein A1
C: Minor capsid protein A1
D: Minor capsid protein A1
E: Minor capsid protein A1
F: Minor capsid protein A1
G: Minor capsid protein A1
H: Minor capsid protein A1
I: Minor capsid protein A1
J: Minor capsid protein A1
K: Minor capsid protein A1
L: Minor capsid protein A1
M: Minor capsid protein A1
N: Minor capsid protein A1
O: Minor capsid protein A1
P: Minor capsid protein A1
Q: Minor capsid protein A1
R: Minor capsid protein A1
S: Minor capsid protein A1
T: Minor capsid protein A1


Theoretical massNumber of molelcules
Total (without water)282,73720
Polymers282,73720
Non-polymers00
Water00
1
A: Minor capsid protein A1
B: Minor capsid protein A1
C: Minor capsid protein A1
D: Minor capsid protein A1
E: Minor capsid protein A1
F: Minor capsid protein A1
G: Minor capsid protein A1
H: Minor capsid protein A1
I: Minor capsid protein A1
J: Minor capsid protein A1
K: Minor capsid protein A1
L: Minor capsid protein A1
M: Minor capsid protein A1
N: Minor capsid protein A1
O: Minor capsid protein A1
P: Minor capsid protein A1
Q: Minor capsid protein A1
R: Minor capsid protein A1
S: Minor capsid protein A1
T: Minor capsid protein A1

A: Minor capsid protein A1
B: Minor capsid protein A1
C: Minor capsid protein A1
D: Minor capsid protein A1
E: Minor capsid protein A1
F: Minor capsid protein A1
G: Minor capsid protein A1
H: Minor capsid protein A1
I: Minor capsid protein A1
J: Minor capsid protein A1
K: Minor capsid protein A1
L: Minor capsid protein A1
M: Minor capsid protein A1
N: Minor capsid protein A1
O: Minor capsid protein A1
P: Minor capsid protein A1
Q: Minor capsid protein A1
R: Minor capsid protein A1
S: Minor capsid protein A1
T: Minor capsid protein A1

A: Minor capsid protein A1
B: Minor capsid protein A1
C: Minor capsid protein A1
D: Minor capsid protein A1
E: Minor capsid protein A1
F: Minor capsid protein A1
G: Minor capsid protein A1
H: Minor capsid protein A1
I: Minor capsid protein A1
J: Minor capsid protein A1
K: Minor capsid protein A1
L: Minor capsid protein A1
M: Minor capsid protein A1
N: Minor capsid protein A1
O: Minor capsid protein A1
P: Minor capsid protein A1
Q: Minor capsid protein A1
R: Minor capsid protein A1
S: Minor capsid protein A1
T: Minor capsid protein A1


Theoretical massNumber of molelcules
Total (without water)848,21260
Polymers848,21260
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area298410 Å2
ΔGint-1995 kcal/mol
Surface area306710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)271.926, 271.926, 166.564
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H
91chain I
101chain J
111chain K
121chain L
131chain M
141chain N
151chain O
161chain P
171chain Q
181chain R
191chain S
201chain T

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 1 - 132 / Label seq-ID: 1 - 132

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF
7chain GGG
8chain HHH
9chain III
10chain JJJ
11chain KKK
12chain LLL
13chain MMM
14chain NNN
15chain OOO
16chain PPP
17chain QQQ
18chain RRR
19chain SSS
20chain TTT

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Components

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


Mass: 14136.874 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus Qbeta / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE1

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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: 4.19 Å3/Da / Density % sol: 70.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 3350, cobalt chloride, Tris / PH range: 8-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→48.1 Å / Num. obs: 57858 / % possible obs: 99.7 % / Redundancy: 2.1 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.7
Reflection shellResolution: 3.5→3.623 Å / Num. unique obs: 5795 / CC1/2: 0.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qbe

1qbe


Resolution: 3.5→48.07 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 2903 5.02 %
Rwork0.1984 54913 -
obs0.2011 57816 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.83 Å2 / Biso mean: 82.9872 Å2 / Biso min: 36.34 Å2
Refinement stepCycle: final / Resolution: 3.5→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19860 0 0 0 19860
Num. residues----2640
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7820X-RAY DIFFRACTION2.274TORSIONAL
12B7820X-RAY DIFFRACTION2.274TORSIONAL
13C7820X-RAY DIFFRACTION2.274TORSIONAL
14D7820X-RAY DIFFRACTION2.274TORSIONAL
15E7820X-RAY DIFFRACTION2.274TORSIONAL
16F7820X-RAY DIFFRACTION2.274TORSIONAL
17G7820X-RAY DIFFRACTION2.274TORSIONAL
18H7820X-RAY DIFFRACTION2.274TORSIONAL
19I7820X-RAY DIFFRACTION2.274TORSIONAL
110J7820X-RAY DIFFRACTION2.274TORSIONAL
111K7820X-RAY DIFFRACTION2.274TORSIONAL
112L7820X-RAY DIFFRACTION2.274TORSIONAL
113M7820X-RAY DIFFRACTION2.274TORSIONAL
114N7820X-RAY DIFFRACTION2.274TORSIONAL
115O7820X-RAY DIFFRACTION2.274TORSIONAL
116P7820X-RAY DIFFRACTION2.274TORSIONAL
117Q7820X-RAY DIFFRACTION2.274TORSIONAL
118R7820X-RAY DIFFRACTION2.274TORSIONAL
119S7820X-RAY DIFFRACTION2.274TORSIONAL
120T7820X-RAY DIFFRACTION2.274TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.560.2819910.28912615270699
3.56-3.620.36071240.30092602272699
3.62-3.680.40111170.277226032720100
3.68-3.750.27151460.260526652811100
3.75-3.830.37221510.267425652716100
3.83-3.910.25791680.247525212689100
3.91-40.27751800.252126842864100
4-4.10.31491280.233726152743100
4.11-4.220.35561320.211126272759100
4.22-4.340.24371420.190226132755100
4.34-4.480.20921780.181626262804100
4.48-4.640.20141080.16126092717100
4.64-4.820.24711040.157226672771100
4.83-5.040.24481400.175626842824100
5.05-5.310.25341280.171125812709100
5.31-5.640.17091480.17725792727100
5.64-6.080.22631560.188726082764100
6.08-6.680.29681000.214526552755100
6.69-7.650.31161560.198226102766100
7.66-9.620.16061560.145726092765100
9.64-48.070.22911500.16662575272598

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