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Yorodumi- PDB-4x4x: Retrofitting antibodies with stabilizing mutations. Herceptin scF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x4x | ||||||
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Title | Retrofitting antibodies with stabilizing mutations. Herceptin scFv mutant. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody stabilization mutations | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å | ||||||
Authors | Langley, D.B. / Roome, B. / Christ, D. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: Retrofitting antibodies with stabilizing mutations Authors: Langley, D.B. / Roome, B. / Christ, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x4x.cif.gz | 167.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x4x.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 4x4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/4x4x ftp://data.pdbj.org/pub/pdb/validation_reports/x4/4x4x | HTTPS FTP |
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-Related 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: 14565.989 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) #2: Antibody | Mass: 11734.021 Da / Num. of mol.: 2 / Mutation: S52D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55 % / Description: small hexagonal rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 3.5 M sodium formate, 100 mM sodium acetate (pH 4.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→35.65 Å / Num. obs: 26621 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.25→35.65 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 20.039 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 44.337 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→35.65 Å
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Refine LS restraints |
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