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Yorodumi- PDB-3hc4: BHA10 IgG1 Fab quadruple mutant variant - antibody directed at hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hc4 | ||||||
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Title | BHA10 IgG1 Fab quadruple mutant variant - antibody directed at human LTBR | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IGG1 FAB / BHA10 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Arndt, J.W. / Jordan, J.L. / Lugovskoy, A. / Wang, D. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules Authors: Jordan, J.L. / Arndt, J.W. / Hanf, K. / Li, G. / Hall, J. / Demarest, S. / Huang, F. / Wu, X. / Miller, B. / Glaser, S. / Fernandez, E.J. / Wang, D. / Lugovskoy, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hc4.cif.gz | 191.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hc4.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hc4_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 3hc4_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 3hc4_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 3hc4_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/3hc4 ftp://data.pdbj.org/pub/pdb/validation_reports/hc/3hc4 | HTTPS FTP |
-Related structure data
Related structure data | 3hc0SC 3hc3C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 22969.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHINESE HAMSTER OVARY (CHO) / Production host: Cricetulus griseus (Chinese hamster) | ||||
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#2: Antibody | Mass: 23288.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHINESE HAMSTER OVARY (CHO) / Production host: Cricetulus griseus (Chinese hamster) | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG 4000, 200 mM calcium acetate 10 mM zinc chloride and 100 mM Tris at pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2008 |
Radiation | Monochromator: diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 66764 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.089 |
Reflection shell | Resolution: 1.62→1.66 Å / Rmerge(I) obs: 0.479 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3HC0 Resolution: 1.62→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.787 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.092 / ESU R Free: 0.071 / 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: 16.133 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.616→1.658 Å / Total num. of bins used: 20
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