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Yorodumi- PDB-7o33: Crystal structure of the anti-PAS Fab 3.1 in complex with its epi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o33 | ||||||
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Title | Crystal structure of the anti-PAS Fab 3.1 in complex with its epitope peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / disordered protein antigen / PAS polypeptide / protein engineering | ||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Schilz, J. / Skerra, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Molecular recognition of structurally disordered Pro/Ala-rich sequences (PAS) by antibodies involves an Ala residue at the hot spot of the epitope. Authors: Schilz, J. / Binder, U. / Friedrich, L. / Gebauer, M. / Lutz, C. / Schlapschy, M. / Schiefner, A. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o33.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o33.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 7o33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o33_validation.pdf.gz | 317.9 KB | Display | wwPDB validaton report |
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Full document | 7o33_full_validation.pdf.gz | 319.8 KB | Display | |
Data in XML | 7o33_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 7o33_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/7o33 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/7o33 | HTTPS FTP |
-Related structure data
Related structure data | 7o2zC 7o30C 7o31SC C: citing same article (ref.) S: Starting model for refinement |
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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: 23972.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 23660.537 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: Protein/peptide | Mass: 1108.159 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: PCA in the peptide sequence is the residue code for pyroglutamic acid Source: (synth.) synthetic construct (others) |
#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: 2.25 Å3/Da / Density % sol: 45.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 200mM LiNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→45.61 Å / Num. obs: 36237 / % possible obs: 97.6 % / Redundancy: 3.019 % / Biso Wilson estimate: 36.495 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.083 / Χ2: 0.932 / Net I/σ(I): 9.21 / Num. measured all: 109397 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7O31 Resolution: 1.85→45.61 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.042 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1673 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.06 Å2 / Biso mean: 42.057 Å2 / Biso min: 21.21 Å2
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Refinement step | Cycle: final / Resolution: 1.85→45.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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