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- PDB-6x6w: Crystal structure of inactive enzymatic binary toxin component fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x6w | ||||||
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Title | Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile | ||||||
![]() | ADP-ribosyltransferase | ||||||
![]() | TOXIN / TRANSFERASE / RIBOSYLTRANSFERASE / CDTA | ||||||
Function / homology | Binary exotoxin A, clostridial type / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / extracellular region / CdtA![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pozharski, E. | ||||||
![]() | ![]() Title: Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile Authors: Pozharski, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.2 KB | Display | ![]() |
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PDB format | ![]() | 77.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6x41C ![]() 2wn4S S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 48276.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG MME2K, 0.1M MIB pH7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→39.12 Å / Num. obs: 36970 / % possible obs: 96.5 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 4.5 % / Num. unique obs: 1488 / CC1/2: 0.18 / % possible all: 60.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WN4 Resolution: 1.89→39.12 Å / Cor.coef. Fo:Fc: 0.9305 / Cor.coef. Fo:Fc free: 0.9081 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.137
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Displacement parameters | Biso max: 171.57 Å2 / Biso mean: 25.73 Å2 / Biso min: 7.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.251 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.89→39.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
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