+Open data
-Basic information
Entry | Database: PDB / ID: 7tjm | ||||||
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Title | Bacteriophage Q beta capsid protein in T3 symmetry | ||||||
Components | Minor capsid protein A1 | ||||||
Keywords | VIRUS LIKE PARTICLE / bacteriophage Q beta capsid / T3 symmetry | ||||||
Function / homology | Read-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 species | Bacteriophage sp. (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å | ||||||
Authors | Jin, X. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tjm.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7tjm.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7tjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/7tjm ftp://data.pdbj.org/pub/pdb/validation_reports/tj/7tjm | HTTPS FTP |
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-Related structure data
Related structure data | 7tjdC 7tjeC 7tjgC 1qbeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: 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 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.18 Å3/Da / Density % sol: 80.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: PEG 3350, cobalt chloride, Tris / PH range: 8.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.54→3.62 Å / Num. unique obs: 17430 / CC1/2: 0.15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 208.92 Å2 / Biso mean: 131.48 Å2 / Biso min: 56.07 Å2
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Refinement step | Cycle: final / Resolution: 3.54→49.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.54→3.632 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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