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Yorodumi- PDB-1iqw: CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE MOUSE ANTI-HUMAN FAS... -
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-Basic information
Entry | Database: PDB / ID: 1iqw | ||||||
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Title | CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE MOUSE ANTI-HUMAN FAS ANTIBODY HFE7A | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / ANTI_FAS / AGONISTIC ANTIBODY / APOPTOSIS | ||||||
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: 2.5 Å | ||||||
Authors | Ito, S. / Takayama, T. / Hanzawa, H. / Ichikawa, K. / Ohsumi, J. / Serizawa, N. / Hata, T. / Haruyama, H. | ||||||
Citation | Journal: J.Biochem. / Year: 2002 Title: Crystal structure of the antigen-binding fragment of apoptosis-inducing mouse anti-human Fas monoclonal antibody HFE7A. Authors: Ito, S. / Takayama, T. / Hanzawa, H. / Ichikawa, K. / Ohsumi, J. / Serizawa, N. / Hata, T. / Haruyama, H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray crystallographic studies on a Fab fragment of the mouse anti-human Fas monoclonal antibody HFE7A Authors: Ito, S. / Takayama, T. / Hanzawa, H. / Ichikawa, K. / Ohsumi, J. / Serizawa, N. / Haruyama, H. / Hata, T. #2: Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 2000 Title: Cloning and expression of a novel murine anti-human Fas antibody Authors: Yoshida-Kato, H. / Ichikawa, K. / Yamaguchi, J. / Watanabe, K. / Ohsumi, J. / Yonehara, S. / Serizawa, N. #3: Journal: INT.IMMUNOL. / Year: 2000 Title: A novel murine anti-human Fas mAb which mitigates lymphadenopathy without hepatotoxicity Authors: Ichikawa, K. / Yoshida-Kato, H. / Ohtsuki, M. / Ohsumi, J. / Yamaguchi, J. / Takahashi, S. / Tani, Y. / Watanabe, M. / Shiraishi, A. / Nishioka, K. / Yonehara, S. / Serizawa, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iqw.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iqw.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 1iqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iqw_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 1iqw_full_validation.pdf.gz | 444.9 KB | Display | |
Data in XML | 1iqw_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 1iqw_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/1iqw ftp://data.pdbj.org/pub/pdb/validation_reports/iq/1iqw | 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: 23919.178 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: FAS-DEFICIENT (FAS-/-) |
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#2: Antibody | Mass: 24886.852 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: FAS-DEFICIENT (FAS-/-) |
#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: 2.2 Å3/Da / Density % sol: 44.1 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: SODIUM CITRATE, SODIUM BORATE, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 296 K / pH: 7.4 / Details: used seeding | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 5, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 15256 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 10.5 / % possible all: 97.8 |
Reflection | *PLUS Num. measured all: 69732 |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / Rfactor obs: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.306 / % reflection Rfree: 8 % / Rfactor Rwork: 0.211 / Rfactor obs: 0.211 |