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- PDB-7tje: Bacteriophage Q beta capsid protein A38K -

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Basic information

Entry
Database: PDB / ID: 7tje
TitleBacteriophage Q beta capsid protein A38K
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 speciesBacteriophage sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 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 / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)70,9755
Polymers70,9755
Non-polymers00
Water2,900161
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
x 12


Theoretical massNumber of molelcules
Total (without water)851,69960
Polymers851,69960
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_564-z,-x+1,y-11
crystal symmetry operation8_566-z,x+1,-y+11
crystal symmetry operation9_465y-1,z+1,x1
crystal symmetry operation10_665-y+1,z+1,-x1
crystal symmetry operation11_465y-1,-z+1,-x1
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area299220 Å2
ΔGint-1974 kcal/mol
Surface area304440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.143, 194.143, 194.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 14194.978 Da / Num. of mol.: 5 / Mutation: A38K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 4.3 Å3/Da / Density % sol: 71.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, L-proline, HEPES / PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.799→45.8 Å / Num. obs: 29445 / % possible obs: 97.9 % / Redundancy: 2 % / CC1/2: 0.8 / Net I/σ(I): 16.5
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 3012 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qbe

1qbe


Resolution: 2.799→45.76 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 1500 5.09 %
Rwork0.2186 27941 -
obs0.2212 29441 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.55 Å2 / Biso mean: 60.3015 Å2 / Biso min: 27.16 Å2
Refinement stepCycle: final / Resolution: 2.799→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4985 0 0 161 5146
Biso mean---51.14 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095060
X-RAY DIFFRACTIONf_angle_d1.126895
X-RAY DIFFRACTIONf_chiral_restr0.061830
X-RAY DIFFRACTIONf_plane_restr0.007910
X-RAY DIFFRACTIONf_dihedral_angle_d4.2613145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.8890.33461520.26862537100
2.889-2.99230.34621500.29342575100
2.9923-3.11210.34141100.27322580100
3.1121-3.25370.34711550.27662562100
3.2537-3.42510.30641310.24592594100
3.4251-3.63970.25561030.2121201678
3.6397-3.92050.27431270.23792575100
3.9205-4.31480.25651370.20762601100
4.3148-4.93850.20571320.16182617100
4.9385-6.21950.26121490.20162599100
6.2195-45.70.24421540.2112685100

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