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Yorodumi- PDB-9axo: Crystal Structure of Antibody HY11-7E1_Ch2 Fab in Complex with Fe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9axo | ||||||
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Title | Crystal Structure of Antibody HY11-7E1_Ch2 Fab in Complex with Fentanyl | ||||||
Components |
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Keywords | IMMUNE SYSTEM / opioids / mAb / fentanyl / cross-reactive | ||||||
Function / homology | Chem-7V7 Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rodarte, J.V. / Pancera, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure-based engineering of monoclonal antibodies against fentanyl and carfentanil for improved binding Authors: Rodarte, J.V. / Pravetoni, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9axo.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9axo.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 9axo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9axo_validation.pdf.gz | 692.4 KB | Display | wwPDB validaton report |
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Full document | 9axo_full_validation.pdf.gz | 696.2 KB | Display | |
Data in XML | 9axo_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 9axo_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/9axo ftp://data.pdbj.org/pub/pdb/validation_reports/ax/9axo | HTTPS FTP |
-Related structure data
Related structure data | 9axnC 9axpC 9axqC 9axrC 9axsC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 25129.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) | ||||||
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#2: Antibody | Mass: 23432.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) | ||||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-7V7 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.4M ammonium sulfate, 0.1M Bis-Tris pH 5.5, 0.01M NiCl2 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.61 Å / Num. obs: 29502 / % possible obs: 100 % / Redundancy: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.04 / Rrim(I) all: 0.056 / Χ2: 1.35 / Net I/σ(I): 20.6 / Num. measured all: 54213 |
Reflection shell | Resolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.262 / Num. measured all: 4460 / Num. unique obs: 2367 / CC1/2: 0.828 / Rpim(I) all: 0.262 / Rrim(I) all: 0.371 / Χ2: 0.58 / Net I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.61 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.08 / 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: 2.1→49.61 Å
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Refine LS restraints |
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LS refinement shell |
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