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Open data
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Basic information
Entry | Database: PDB / ID: 8dab | |||||||||
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Title | Coevolved affibody-Z domain pair LL2.c17 | |||||||||
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![]() | PROTEIN BINDING / affibody | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jude, K.M. / Yang, A. / Garcia, K.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Deploying synthetic coevolution and machine learning to engineer protein-protein interactions. Authors: Yang, A. / Jude, K.M. / Lai, B. / Minot, M. / Kocyla, A.M. / Glassman, C.R. / Nishimiya, D. / Kim, Y.S. / Reddy, S.T. / Khan, A.A. / Garcia, K.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.3 KB | Display | ![]() |
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PDB format | ![]() | 61.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8da3C ![]() 8da4C ![]() 8da5C ![]() 8da6C ![]() 8da7C ![]() 8da8C ![]() 8da9C ![]() 8daaC ![]() 8dacC ![]() 5djtS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 7855.707 Da / Num. of mol.: 1 / Mutation: Q9V, G29A, I31V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 7672.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 2.3 M Amm2HPO4, 100 mM Tris pH 8.2 cryoprotected in 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.77488 Å / Relative weight: 1 |
Reflection | Resolution: 1.134→31.65 Å / Num. obs: 27318 / % possible obs: 60.77 % / Redundancy: 9.8 % / Biso Wilson estimate: 12.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09152 / Rpim(I) all: 0.03031 / Rrim(I) all: 0.09654 / Net I/σ(I): 15.86 |
Reflection shell | Resolution: 1.134→1.175 Å / Redundancy: 9.4 % / Rmerge(I) obs: 4.141 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 140 / CC1/2: 0.321 / CC star: 0.697 / Rpim(I) all: 1.415 / Rrim(I) all: 4.383 / % possible all: 3.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5djt Resolution: 1.134→31.65 Å / SU ML: 0.1067 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7765 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.134→31.65 Å
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Refine LS restraints |
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LS refinement shell |
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