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Yorodumi- PDB-2fat: An anti-urokinase plasminogen activator receptor (UPAR) antibody:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fat | ||||||
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Title | An anti-urokinase plasminogen activator receptor (UPAR) antibody: Crystal structure and binding epitope | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTI-UPAR ANTIBODY / ATN-615 / FAB | ||||||
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: 1.77 Å | ||||||
Authors | Li, Y. / Parry, G. / Shi, X. / Chen, L. / Callahan, J.A. / Mazar, A.P. / Huang, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: An anti-urokinase plasminogen activator receptor (uPAR) antibody: crystal structure and binding epitope Authors: Li, Y. / Parry, G. / Chen, L. / Callahan, J.A. / Shaw, D.E. / Meehan, E.J. / Mazar, A.P. / Huang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fat.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fat.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 2fat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fat_validation.pdf.gz | 423.5 KB | Display | wwPDB validaton report |
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Full document | 2fat_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 2fat_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 2fat_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/2fat ftp://data.pdbj.org/pub/pdb/validation_reports/fa/2fat | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23269.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23041.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: 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: 2.27 Å3/Da / Density % sol: 45.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 28%(w/v) PEG 3350, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Oct 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→40.29 Å / Num. obs: 41141 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.77→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2 / % possible all: 58.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→40.29 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 552172.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.6582 Å2 / ksol: 0.345433 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.77→40.29 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.77→1.81 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
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Xplor file |
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