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- PDB-6ro0: CRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT. -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ro0 | ||||||
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Title | CRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT. | ||||||
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![]() | TOXIN | ||||||
Function / homology | ![]() Transferases; Glycosyltransferases; Pentosyltransferases / : / NAD+-protein poly-ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / host cell plasma membrane / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bertrand, T. | ||||||
![]() | ![]() Title: Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity. Authors: Ausar, S.F. / Zhu, S. / Duprez, J. / Cohen, M. / Bertrand, T. / Steier, V. / Wilson, D.J. / Li, S. / Sheung, A. / Brookes, R.H. / Pedyczak, A. / Rak, A. / Andrew James, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 393.2 KB | Display | ![]() |
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PDB format | ![]() | 311.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 545.6 KB | Display | ![]() |
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Full document | ![]() | 574.7 KB | Display | |
Data in XML | ![]() | 68 KB | Display | |
Data in CIF | ![]() | 95.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1prtS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Pertussis toxin subunit ... , 2 types, 4 molecules AGFL
#1: Protein | Mass: 29905.109 Da / Num. of mol.: 2 / Mutation: R9K, E129G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Protein | Mass: 14513.755 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ptxE, ERS004697_00105, ERS004704_00093, ERS004709_00175, ERS005128_00197, ERS005179_00180, ERS014547_00748, ERS014550_01624, ERS018341_00090 Production host: ![]() |
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-Islet-activating protein ... , 3 types, 8 molecules BHCIDEJK
#2: Protein | Mass: 24856.299 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ptxB, CYO81_20230, ERS004697_00332, ERS004704_00067, ERS004709_00223, ERS005128_00199, ERS005179_00182, ERS014547_00750, NCTC10911_00247 Production host: ![]() #3: Protein | Mass: 25012.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ptxS3, ptxC, ptxC_1, ptxC_2, CYO81_20245, ERS004697_00106, ERS004704_00094, ERS004709_00174, ERS005128_00196, ERS005179_00179, ERS014547_00747, ERS014550_01623, NCTC10911_00250 Production host: ![]() #4: Protein | Mass: 16566.744 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ptxD, CYO81_20235, ERS005128_00198, ERS005179_00181, ERS014547_00749, NCTC10911_00248 Production host: ![]() |
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-Non-polymers , 2 types, 533 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.63 % |
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Crystal grow | Temperature: 278 K / Method: evaporation / pH: 7 / Details: Spontaneous crystallization in plastic bottles / PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→46.96 Å / Num. obs: 165565 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 50.68 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.13→2.2 Å / Rmerge(I) obs: 1.95 / Num. unique obs: 16119 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PRT Resolution: 2.13→46.62 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.89 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.192 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.167
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Displacement parameters | Biso mean: 64.94 Å2
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Refine analyze | Luzzati coordinate error obs: 0.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→46.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.19 Å / Total num. of bins used: 20
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