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Yorodumi- PDB-6k4z: Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k4z | ||||||
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Title | Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID | ||||||
Components | scFv of C6 | ||||||
Keywords | IMMUNE SYSTEM / antigen binding / affinity maturation / Somatic hypermutation / conformational change | ||||||
Function / homology | 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Nishiguchi, A. / Numoto, N. / Ito, N. / Azuma, T. / Oda, M. | ||||||
Citation | Journal: Mol.Immunol. / Year: 2019 Title: Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain. Authors: Nishiguchi, A. / Numoto, N. / Ito, N. / Azuma, T. / Oda, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k4z.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k4z.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 6k4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k4z_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6k4z_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6k4z_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 6k4z_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/6k4z ftp://data.pdbj.org/pub/pdb/validation_reports/k4/6k4z | HTTPS FTP |
-Related structure data
Related structure data | 3et9S S: Starting model for refinement |
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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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-Components
#1: Antibody | Mass: 26116.920 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The fusion protein of expression tags (residues -2-0), the light chain (residues 1-108), linker GGGGSGGGGSGGGGS (residues 501-515), and the heavy chain (residues 1001-1113) Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-32TH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): codon plus #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.14 M Lithium sulfate monohydrate, 0.07 M TRIS hydrochloride pH 8.5, 21% w/v Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 12, 2018 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 52628 / % possible obs: 96.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.07 Å2 / CC1/2: 0.998 / Rsym value: 0.073 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 3.5 % / Num. unique obs: 8339 / CC1/2: 0.716 / Rsym value: 0.586 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ET9 Resolution: 1.65→43.29 Å / SU ML: 0.173 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.1576
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→43.29 Å
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Refine LS restraints |
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LS refinement shell |
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