+Open data
-Basic information
Entry | Database: PDB / ID: 6pe7 | ||||||
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Title | Crystal Structure of ABBV-323 FAB | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CD40 / FAB | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Argiriadi, M.A. | ||||||
Citation | Journal: BMC Mol Cell Biol / Year: 2019 Title: CD40/anti-CD40 antibody complexes which illustrate agonist and antagonist structural switches. Authors: Argiriadi, M.A. / Benatuil, L. / Dubrovska, I. / Egan, D.A. / Gao, L. / Greischar, A. / Hardman, J. / Harlan, J. / Iyer, R.B. / Judge, R.A. / Lake, M. / Perron, D.C. / Sadhukhan, R. / ...Authors: Argiriadi, M.A. / Benatuil, L. / Dubrovska, I. / Egan, D.A. / Gao, L. / Greischar, A. / Hardman, J. / Harlan, J. / Iyer, R.B. / Judge, R.A. / Lake, M. / Perron, D.C. / Sadhukhan, R. / Sielaff, B. / Sousa, S. / Wang, R. / McRae, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pe7.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pe7.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 6pe7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pe7_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 6pe7_full_validation.pdf.gz | 442.9 KB | Display | |
Data in XML | 6pe7_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 6pe7_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/6pe7 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/6pe7 | HTTPS FTP |
-Related structure data
Related structure data | 6pe8C 6pe9C 3qos S: Starting model for refinement C: citing same article (ref.) |
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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: Antibody | Mass: 23748.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) | ||||||
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#2: Antibody | Mass: 24290.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.06 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion Details: 25% (w/v) PMME 550, 0.1M MES pH 6.5, 0.01M zinc sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→57.2 Å / Num. obs: 56956 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.74→1.75 Å / Num. unique obs: 545 / CC1/2: 0.793 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QOS 3qos Resolution: 1.74→24.356 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 22.71 / Stereochemistry target values: MLHL
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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: 1.74→24.356 Å
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Refine LS restraints |
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LS refinement shell |
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