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- PDB-7tjg: Bacteriophage Q beta capsid protein, A38K/A40C/D102C in T1 symmetry -

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Basic information

Entry
Database: PDB / ID: 7tjg
TitleBacteriophage Q beta capsid protein, A38K/A40C/D102C in T1 symmetry
ComponentsMinor capsid protein A1
KeywordsVIRUS LIKE PARTICLE / bacteriophage Q beta capsid / T1 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: 3.903 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 1.2Nov 6, 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
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)71,0755
Polymers71,0755
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
x 12


Theoretical massNumber of molelcules
Total (without water)852,90660
Polymers852,90660
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area306910 Å2
ΔGint-2229 kcal/mol
Surface area313100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.690, 191.690, 191.690
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: 14215.099 Da / Num. of mol.: 5 / Mutation: A38K, A40C, D102C
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: 4.13 Å3/Da / Density % sol: 70.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 3350, L-proline, HEPES / PH range: 7.0-7.5

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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 16M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.9→30.3 Å / Num. obs: 10727 / % possible obs: 98.8 % / Redundancy: 30.6 % / CC1/2: 0.503 / Net I/σ(I): 10.3
Reflection shellResolution: 3.9→3.97 Å / Num. unique obs: 1074 / CC1/2: 0.503

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Processing

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

1qbe


Resolution: 3.903→30.3 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2818 523 4.89 %
Rwork0.2162 10181 -
obs0.2194 10704 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.36 Å2 / Biso mean: 120.7138 Å2 / Biso min: 80.37 Å2
Refinement stepCycle: final / Resolution: 3.903→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 0 0 4980
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045054
X-RAY DIFFRACTIONf_angle_d0.7286883
X-RAY DIFFRACTIONf_chiral_restr0.046830
X-RAY DIFFRACTIONf_plane_restr0.008905
X-RAY DIFFRACTIONf_dihedral_angle_d2.8123145
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.9031-4.29510.35261320.28082541100
4.2951-4.91460.24571360.21062538100
4.9146-6.18450.27261120.21832579100
6.1845-30.30.28331430.196252397

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