+Open data
-Basic information
Entry | Database: PDB / ID: 4qth | ||||||
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Title | Crystal structure of anti-uPAR Fab 8B12 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Zhao, B. / Yuan, C. / Luo, Z. / Huang, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Stabilizing a flexible interdomain hinge region harboring the SMB binding site drives uPAR into its closed conformation. Authors: Zhao, B. / Gandhi, S. / Yuan, C. / Luo, Z. / Li, R. / Gardsvoll, H. / de Lorenzi, V. / Sidenius, N. / Huang, M. / Ploug, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qth.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qth.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 4qth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/4qth ftp://data.pdbj.org/pub/pdb/validation_reports/qt/4qth | HTTPS FTP |
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-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: 24032.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 23642.959 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #3: 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: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 18%(w/v) PEG3350, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→41.31 Å / Num. obs: 50246 / % possible obs: 99.6 % / Redundancy: 7.3 % |
Reflection shell | Resolution: 2.17→2.23 Å / Redundancy: 7.5 % / Num. unique all: 3707 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→41.31 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.879 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 52.103 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→41.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.226 Å / Total num. of bins used: 20
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