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Yorodumi- PDB-6x6x: Crystal structure of enzymatic binary toxin component from Clostr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x6x | ||||||
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Title | Crystal structure of enzymatic binary toxin component from Clostridium difficile in complex with | ||||||
Components | ADP-ribosyltransferase | ||||||
Keywords | 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 / Chem-UTG / CdtA Function and homology information | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Pozharski, E. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of enzymatic binary toxin component from Clostridium difficile in complex with Authors: Pozharski, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x6x.cif.gz | 190.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x6x.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 6x6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x6x_validation.pdf.gz | 814.5 KB | Display | wwPDB validaton report |
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Full document | 6x6x_full_validation.pdf.gz | 821.7 KB | Display | |
Data in XML | 6x6x_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 6x6x_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/6x6x ftp://data.pdbj.org/pub/pdb/validation_reports/x6/6x6x | HTTPS FTP |
-Related structure data
Related structure data | 2wn4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48276.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cdtA / Production host: Escherichia coli (E. coli) / References: UniProt: F5B5W8 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-UTG / | #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.31 Å3/Da / Density % sol: 46.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium Thiocyanate, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→40 Å / Num. obs: 96532 / % possible obs: 99.4 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rpim(I) all: 0.042 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.71→1.74 Å / Num. unique obs: 4729 / CC1/2: 0.364 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2wn4 Resolution: 1.71→39.44 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9323 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.106
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Displacement parameters | Biso max: 104.87 Å2 / Biso mean: 29.75 Å2 / Biso min: 10.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.71→39.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.75 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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