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Yorodumi- PDB-7ce2: The Crystal structure of TeNT Hc complexed with neutralizing antibody -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ce2 | ||||||
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Title | The Crystal structure of TeNT Hc complexed with neutralizing antibody | ||||||
Components |
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Keywords | HYDROLASE / antibody | ||||||
Function / homology | Function and homology information negative regulation of neurotransmitter secretion / : / metallopeptidase activity / extracellular region Similarity search - Function | ||||||
Biological species | Clostridium tetani (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Wang, X. / Wang, Y. / Wu, C. / Yu, J. / Liao, H. | ||||||
Citation | Journal: Cell Rep / Year: 2021 Title: Structural basis of tetanus toxin neutralization by native human monoclonal antibodies. Authors: Wang, Y. / Wu, C. / Yu, J. / Lin, S. / Liu, T. / Zan, L. / Li, N. / Hong, P. / Wang, X. / Jia, Z. / Li, J. / Wang, Y. / Zhang, M. / Yuan, X. / Li, C. / Xu, W. / Zheng, W. / Wang, X. / Liao, H.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ce2.cif.gz | 369.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ce2.ent.gz | 300.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ce2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ce2_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 7ce2_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 7ce2_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 7ce2_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/7ce2 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/7ce2 | HTTPS FTP |
-Related structure data
Related structure data | 1a8dS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52838.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium tetani (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LA13 |
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#2: Antibody | Mass: 23926.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 23421.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.12 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, sitting drop Details: 3% w/v Dextran sulfate (sodium salt), 0.1M BICINE PH 8.5, 15% w/v PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→38.067 Å / Num. obs: 75830 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 40.44 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.01→2.12 Å / Num. unique obs: 75830 / CC1/2: 0.996 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A8D Resolution: 2.01→38.067 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.38 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.75 Å2 / Biso mean: 54.7428 Å2 / Biso min: 26.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.01→38.067 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 61.2251 Å / Origin y: 155.357 Å / Origin z: 286.6931 Å
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Refinement TLS group |
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