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- PDB-4dvb: The crystal structure of the Fab fragment of pro-uPA antibody mAb-112 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dvb | ||||||
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Title | The crystal structure of the Fab fragment of pro-uPA antibody mAb-112 | ||||||
![]() | (Fab fragment of pro-uPA antibody mAb-112) x 2 | ||||||
![]() | IMMUNE SYSTEM / HYDROLASE | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, L. / Botkjaer, K.A. / Andersen, L.M. / Yuan, C. / Andreasen, P.A. / Huang, M. | ||||||
![]() | ![]() Title: Rezymogenation of active urokinase induced by an inhibitory antibody. Authors: Jiang, L. / Botkjaer, K.A. / Andersen, L.M. / Yuan, C. / Andreasen, P.A. / Huang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.4 KB | Display | ![]() |
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PDB format | ![]() | 148.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.4 KB | Display | ![]() |
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Full document | ![]() | 486.6 KB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 55.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23003.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Antibody | Mass: 23599.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PG4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 2.3M ammonium sulfate, 100mM Tris-HCl (pH 7.4), 5% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→77.67 Å / Num. obs: 67906 / % possible obs: 98.52 % / Redundancy: 9.9 % |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 7.4 % / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.998 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→77.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.933→1.983 Å / Total num. of bins used: 20
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