+Open data
-Basic information
Entry | Database: PDB / ID: 8dac | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Coevolved affibody-Z domain pair LL2.c22 | |||||||||
Components |
| |||||||||
Keywords | PROTEIN BINDING / affibody | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Staphylococcus aureus (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | |||||||||
Authors | Jude, K.M. / Yang, A. / Garcia, K.C. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Science / Year: 2023 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8dac.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8dac.ent.gz | 62.2 KB | Display | PDB format |
PDBx/mmJSON format | 8dac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dac_validation.pdf.gz | 448.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8dac_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 8dac_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 8dac_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/8dac ftp://data.pdbj.org/pub/pdb/validation_reports/da/8dac | HTTPS FTP |
-Related structure data
Related structure data | 8da3C 8da4C 8da5C 8da6C 8da7C 8da8C 8da9C 8daaC 8dabC 5djtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/929 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Antibody | Mass: 7850.663 Da / Num. of mol.: 1 / Mutation: Q9I, F13V, L17F, G29A, I31F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P38507 |
---|---|
#2: Protein | Mass: 7643.584 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.53 Å3/Da / Density % sol: 19.62 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 2.5 M AmmSO4, 100 mM Tris pH 8.2 Cryoprotected with 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→36.93 Å / Num. obs: 28352 / % possible obs: 94.27 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.66 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06903 / Rpim(I) all: 0.0289 / Rrim(I) all: 0.07499 / Net I/σ(I): 12.62 |
Reflection shell | Resolution: 1.19→1.233 Å / Redundancy: 5.3 % / Rmerge(I) obs: 2.251 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 2038 / CC1/2: 0.365 / CC star: 0.731 / Rpim(I) all: 1.053 / Rrim(I) all: 2.494 / % possible all: 66.45 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5djt Resolution: 1.19→36.93 Å / SU ML: 0.1902 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4665 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.19→36.93 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|