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- PDB-1s5d: Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s5d | ||||||
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Title | Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 2 | ||||||
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![]() | TRANSFERASE / TOXIN / cholera toxin / heat-labile enterotoxin / ADP ribose transferases / AB5 toxins | ||||||
Function / homology | ![]() host cell surface binding / galactose binding / glycosyltransferase activity / catalytic complex / Transferases; Glycosyltransferases; Pentosyltransferases / localization / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / toxin activity / periplasmic space ...host cell surface binding / galactose binding / glycosyltransferase activity / catalytic complex / Transferases; Glycosyltransferases; Pentosyltransferases / localization / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding / host cell plasma membrane / extracellular space / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | O'Neal, C.J. / Amaya, E.I. / Jobling, M.G. / Holmes, R.K. / Hol, W.G. | ||||||
![]() | ![]() Title: Crystal structures of an intrinsically active cholera toxin mutant yield insight into the toxin activation mechanism Authors: O'Neal, C.J. / Amaya, E.I. / Jobling, M.G. / Holmes, R.K. / Hol, W.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.2 KB | Display | ![]() |
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PDB format | ![]() | 131.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.7 KB | Display | ![]() |
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Full document | ![]() | 502.4 KB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 49.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1s5bSC ![]() 1s5cC ![]() 1s5eC ![]() 1s5fC 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
-Protein , 2 types, 6 molecules ADEFGH
#1: Protein | Mass: 27152.875 Da / Num. of mol.: 1 / Mutation: Y30S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P01555, NAD+-diphthamide ADP-ribosyltransferase |
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#2: Protein | Mass: 11623.267 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 1 types, 5 molecules ![](data/chem/img/GAL.gif)
#5: Sugar | ChemComp-GAL / |
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-Non-polymers , 3 types, 609 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NA / | ||
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#4: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: PEG 3350, sodium citrate, galactose, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 28, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→38.92 Å / Num. all: 81705 / Num. obs: 81705 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rsym value: 0.068 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.75→1.81 Å / Mean I/σ(I) obs: 3.37 / Num. unique all: 6191 / Rsym value: 0.291 / % possible all: 73.2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: CTY30S Form 3 structure (PDB ID 1S5B) Resolution: 1.75→30.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.973 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.561 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20 /
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