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Yorodumi- PDB-7tjg: Bacteriophage Q beta capsid protein, A38K/A40C/D102C in T1 symmetry -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tjg | ||||||
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Title | Bacteriophage Q beta capsid protein, A38K/A40C/D102C in T1 symmetry | ||||||
Components | Minor capsid protein A1 | ||||||
Keywords | VIRUS LIKE PARTICLE / bacteriophage Q beta capsid / T1 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: 3.903 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 | 7tjg.cif.gz | 133.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tjg.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 7tjg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/7tjg ftp://data.pdbj.org/pub/pdb/validation_reports/tj/7tjg | HTTPS FTP |
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-Related structure data
Related structure data | 7tjdC 7tjeC 7tjmC 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: 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 |
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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: 4.13 Å3/Da / Density % sol: 70.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 3350, L-proline, HEPES / PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→30.3 Å / Num. obs: 10727 / % possible obs: 98.8 % / Redundancy: 30.6 % / CC1/2: 0.503 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.9→3.97 Å / Num. unique obs: 1074 / CC1/2: 0.503 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.36 Å2 / Biso mean: 120.7138 Å2 / Biso min: 80.37 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.903→30.3 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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