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Yorodumi- PDB-7o30: Crystal structure of the anti-PAS Fab 1.1 in complex with its epi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o30 | ||||||
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Title | Crystal structure of the anti-PAS Fab 1.1 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: 2.65 Å | ||||||
Authors | Schilz, J. / Schiefner, A. / 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 | 7o30.cif.gz | 181.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o30.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 7o30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/7o30 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/7o30 | HTTPS FTP |
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-Related structure data
Related structure data | 7o2zSC 7o31C 7o33C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Antibody | Mass: 23977.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 24723.697 Da / Num. of mol.: 2 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: 862.925 Da / Num. of mol.: 2 / 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 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% (w/v) PEG 3350 100 mM HEPES pH 7.5 200 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 27, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→34.13 Å / Num. obs: 30855 / % possible obs: 96.9 % / Redundancy: 22.197 % / Biso Wilson estimate: 63.305 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.112 / Χ2: 0.87 / Net I/σ(I): 24.34 / Num. measured all: 684889 / Scaling rejects: 1117 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 7O2Z Resolution: 2.65→34.13 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.506 / SU ML: 0.302 / SU R Cruickshank DPI: 1.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.105 / ESU R Free: 0.353 / 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: 169.14 Å2 / Biso mean: 67.467 Å2 / Biso min: 30.91 Å2
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Refinement step | Cycle: final / Resolution: 2.65→34.13 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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