+Open data
-Basic information
Entry | Database: PDB / ID: 8da8 | |||||||||
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Title | Coevolved affibody-Z domain pair LL2.c1 | |||||||||
Components |
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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: 1.29 Å | |||||||||
Authors | Jude, K.M. / Yang, A. / Garcia, K.C. | |||||||||
Funding support | United States, 2items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8da8.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8da8.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 8da8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8da8_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 8da8_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 8da8_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 8da8_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/8da8 ftp://data.pdbj.org/pub/pdb/validation_reports/da/8da8 | HTTPS FTP |
-Related structure data
Related structure data | 8da3C 8da4C 8da5C 8da6C 8da7C 8da9C 8daaC 8dabC 8dacC 5djtS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/925 / Data set type: diffraction image data |
-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: 7761.548 Da / Num. of mol.: 1 / Mutation: Q9L F13V, 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 |
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#2: Protein | Mass: 7727.726 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 |
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-Sample preparation
Crystal | Density Matthews: 1.52 Å3/Da / Density % sol: 19.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.5 M ammonium sulfate 100 mM HEPES pH 7.0 Cryoprotected with 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.82653 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: 0.82653 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→26.46 Å / Num. obs: 22160 / % possible obs: 94.39 % / Redundancy: 7.1 % / Biso Wilson estimate: 15.99 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06021 / Rpim(I) all: 0.02429 / Rrim(I) all: 0.06502 / Net I/σ(I): 17.31 |
Reflection shell | Resolution: 1.29→1.336 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.304 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 2223 / CC1/2: 0.824 / CC star: 0.951 / Rpim(I) all: 0.5168 / Rrim(I) all: 1.404 / % possible all: 94.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5djt Resolution: 1.29→26.46 Å / SU ML: 0.1792 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1255 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: 22.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→26.46 Å
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Refine LS restraints |
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LS refinement shell |
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