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Open data
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Basic information
Entry | Database: PDB / ID: 7duo | ||||||
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Title | Crystal structure of daratumumab fab and CD38 complex | ||||||
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Function / homology | ![]() 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, X.J. / Wang, L. / Yu, C.F. | ||||||
![]() | ![]() Title: Crystal structure of daratumumab fab and CD38 complex Authors: Yu, X.J. / Wang, L. / Yu, C.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259.9 KB | Display | ![]() |
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PDB format | ![]() | 209.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1yh3S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | ![]() Mass: 23595.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 26650.408 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase |
#3: Antibody | ![]() Mass: 23302.799 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.96 % |
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Crystal grow![]() | Temperature: 291 K / Method: evaporation, recrystallization Details: 0.2M Sodium phosphate monobasic monohydrate, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.81→50 Å / Num. obs: 19416 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.969 / Rmerge(I) obs: 0.183 / Net I/σ(I): 12.18 |
Reflection shell | Resolution: 2.81→2.9 Å / Rmerge(I) obs: 0.183 / Num. unique obs: 19416 / CC1/2: 0.969 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1yh3 Resolution: 2.81→46.055 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.5 / 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: 124.93 Å2 / Biso mean: 36.1454 Å2 / Biso min: 7.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.81→46.055 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 39.1934 Å / Origin y: 30.0133 Å / Origin z: 21.1732 Å
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Refinement TLS group |
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