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- PDB-4u6v: Mechanisms of Neutralization of a Human Anti-Alpha Toxin Antibody -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u6v | |||||||||
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Title | Mechanisms of Neutralization of a Human Anti-Alpha Toxin Antibody | |||||||||
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![]() | IMMUNE SYSTEM / alpha toxin / Fab / Staphylococcus aureus / mutagenesis | |||||||||
Function / homology | ![]() hemolysis in another organism / : / toxin activity / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Oganesyan, V.Y. / Peng, L. / Damschroder, M.M. / Cheng, L. / Sadowska, A. / Tkaczyk, C. / Sellman, B. / Wu, H. / Dall'Acqua, W.F. | |||||||||
![]() | ![]() Title: Mechanisms of Neutralization of a Human Anti-alpha-toxin Antibody. Authors: Oganesyan, V. / Peng, L. / Damschroder, M.M. / Cheng, L. / Sadowska, A. / Tkaczyk, C. / Sellman, B.R. / Wu, H. / Dall'Acqua, W.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 561.5 KB | Display | ![]() |
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PDB format | ![]() | 465.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.6 KB | Display | ![]() |
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Full document | ![]() | 496.4 KB | Display | |
Data in XML | ![]() | 48.2 KB | Display | |
Data in CIF | ![]() | 66.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ahlS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Antibody | Mass: 23794.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #2: Antibody | Mass: 23404.002 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #3: Protein | Mass: 33302.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Diffraction quality crystals grew in about a week in hanging drops where 3 ul of the MEDI4893 Fab/AT complex at a concentration of 15 mg/ml in 50 mM Tris-HCl, pH 7.5, 100 mM NaCl was mixed ...Details: Diffraction quality crystals grew in about a week in hanging drops where 3 ul of the MEDI4893 Fab/AT complex at a concentration of 15 mg/ml in 50 mM Tris-HCl, pH 7.5, 100 mM NaCl was mixed with 2 ul of 10% (w/v) PEG 6000, 100 mM HEPES, pH 7.0 and let to equilibrate against 300 ul of 10% (w/v) PEG 6000, 100 mM HEPES, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→92.45 Å / Num. obs: 74008 / % possible obs: 97.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.56→2.75 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1.3 / % possible all: 98.6 |
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Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 7AHL Resolution: 2.56→92.45 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 25.384 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.455 Å2
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Refinement step | Cycle: 1 / Resolution: 2.56→92.45 Å
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Refine LS restraints |
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