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Yorodumi- PDB-4p2c: Complex of Shiga toxin 2e with a neutralizing single-domain antibody -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p2c | ||||||
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Title | Complex of Shiga toxin 2e with a neutralizing single-domain antibody | ||||||
Components |
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Keywords | TOXIN / Nanobody / Complex / Lectin | ||||||
Function / homology | Function and homology information hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / toxin activity / blood microparticle / negative regulation of translation / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.818 Å | ||||||
Authors | Lo, A.W.H. / Moonens, K. / De Kerpel, M. / Brys, L. / Pardon, E. / Remaut, H. / De Greve, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: The Molecular Mechanism of Shiga Toxin Stx2e Neutralization by a Single-domain Antibody Targeting the Cell Receptor-binding Domain. Authors: Lo, A.W. / Moonens, K. / De Kerpel, M. / Brys, L. / Pardon, E. / Remaut, H. / De Greve, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p2c.cif.gz | 241.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p2c.ent.gz | 195.3 KB | Display | PDB format |
PDBx/mmJSON format | 4p2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p2c_validation.pdf.gz | 494.8 KB | Display | wwPDB validaton report |
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Full document | 4p2c_full_validation.pdf.gz | 515.4 KB | Display | |
Data in XML | 4p2c_validation.xml.gz | 41 KB | Display | |
Data in CIF | 4p2c_validation.cif.gz | 57.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/4p2c ftp://data.pdbj.org/pub/pdb/validation_reports/p2/4p2c | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33011.961 Da / Num. of mol.: 1 / Mutation: Y99S, E189Q, K296T, P313S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WUF4 | ||
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#2: Protein | Mass: 7590.478 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: stxB2e, orf, stx2e B, stx2eB / Production host: Escherichia coli (E. coli) / References: UniProt: Q47644 #3: Antibody | Mass: 14196.622 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / References: UniProt: R9VYW2 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.5 ?L sitting drops and a complex-to-well solution (0.5 M succinic acid pH 7.0, 0.1M Bis-Tris propane pH 7.0) ratio of 1:1 (v/v). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray / Wavelength: 0.98 |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.818→44.1 Å / Num. obs: 42054 / % possible obs: 99.9 % / Redundancy: 6 % / Net I/σ(I): 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.818→43.714 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.818→43.714 Å
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Refine LS restraints |
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LS refinement shell |
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