+Open data
-Basic information
Entry | Database: PDB / ID: 8s4h | ||||||||||||
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Title | Crystal structure of scFv-1B6 in complex with rocuronium bromide | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / NeuroMuscular Blocking Agents Rocuronium-induced anaphylaxis | ||||||||||||
Function / homology | rocuronium Function and homology information | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Saul, F.A. / Haouz, A. / Bruhns, P. | ||||||||||||
Funding support | France, European Union, 3items
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Citation | Journal: Sci Transl Med / Year: 2024 Title: Rocuronium-specific antibodies drive perioperative anaphylaxis but can also function as reversal agents in preclinical models. Authors: Dejoux, A. / Zhu, Q. / Ganneau, C. / Goff, O.R. / Godon, O. / Lemaitre, J. / Relouzat, F. / Huetz, F. / Sokal, A. / Vandenberghe, A. / Pecalvel, C. / Hunault, L. / Derenne, T. / Gillis, C.M. ...Authors: Dejoux, A. / Zhu, Q. / Ganneau, C. / Goff, O.R. / Godon, O. / Lemaitre, J. / Relouzat, F. / Huetz, F. / Sokal, A. / Vandenberghe, A. / Pecalvel, C. / Hunault, L. / Derenne, T. / Gillis, C.M. / Iannascoli, B. / Wang, Y. / Rose, T. / Mertens, C. / Nicaise-Roland, P. / England, P. / Mahevas, M. / de Chaisemartin, L. / Le Grand, R. / Letscher, H. / Saul, F. / Pissis, C. / Haouz, A. / Reber, L.L. / Chappert, P. / Jonsson, F. / Ebo, D.G. / Millot, G.A. / Bay, S. / Chollet-Martin, S. / Gouel-Cheron, A. / Bruhns, P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s4h.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s4h.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 8s4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8s4h_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8s4h_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8s4h_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 8s4h_validation.cif.gz | 59.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/8s4h ftp://data.pdbj.org/pub/pdb/validation_reports/s4/8s4h | HTTPS FTP |
-Related structure data
Related structure data | 8s4kC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Antibody | Mass: 17426.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 13648.019 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila (fruit flies) #3: Chemical | #4: 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 grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30%(v/v) PEG400 0.1M MES pH6.5 0.1 M Na Acetate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980112 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→127.52 Å / Num. obs: 156312 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.027 / Rrim(I) all: 0.084 / Χ2: 1.02 / Net I/σ(I): 16.4 / Num. measured all: 1501870 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 1.707 / Num. measured all: 70880 / Num. unique obs: 7680 / CC1/2: 0.567 / Rpim(I) all: 0.594 / Rrim(I) all: 1.808 / Χ2: 1.04 / Net I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50.01 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.724 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.066 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.707 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→50.01 Å
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Refine LS restraints |
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