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Yorodumi- PDB-4dvb: The crystal structure of the Fab fragment of pro-uPA antibody mAb-112 -
+Open data
-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 | ||||||
Components | (Fab fragment of pro-uPA antibody mAb-112) x 2 | ||||||
Keywords | IMMUNE SYSTEM / HYDROLASE | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å | ||||||
Authors | Jiang, L. / Botkjaer, K.A. / Andersen, L.M. / Yuan, C. / Andreasen, P.A. / Huang, M. | ||||||
Citation | Journal: Biochem.J. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dvb.cif.gz | 179.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dvb.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 4dvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dvb_validation.pdf.gz | 476.4 KB | Display | wwPDB validaton report |
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Full document | 4dvb_full_validation.pdf.gz | 486.6 KB | Display | |
Data in XML | 4dvb_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 4dvb_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/4dvb ftp://data.pdbj.org/pub/pdb/validation_reports/dv/4dvb | HTTPS FTP |
-Related structure data
-Links
-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) Mus musculus (house mouse) #2: Antibody | Mass: 23599.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PG4 / | #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: 2.57 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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.93→77.67 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.988 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.166 / 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: 1.4 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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