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Yorodumi- PDB-1pg7: Murine 6A6 Fab in complex with humanized anti-Tissue Factor D3H44 Fab -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pg7 | ||||||
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Title | Murine 6A6 Fab in complex with humanized anti-Tissue Factor D3H44 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Eigenbrot, C. / Meng, Y.G. / Krishnamurthy, R. / Lipari, M.T. / Presta, L. / Devaux, B. / Wong, T. / Moran, P. / Bullens, S. / Kirchhofer, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural insight into how an anti-idiotypic antibody against D3H44 (anti-tissue factor antibody) restores normal coagulation. Authors: Eigenbrot, C. / Meng, Y.G. / Krishnamurthy, R. / Lipari, M.T. / Presta, L. / Devaux, B. / Wong, T. / Moran, P. / Bullens, S. / Kirchhofer, D. | ||||||
History |
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Remark 600 | HETEROGEN SOLVENT ATOMS NUMBERED 1 - 125 ARE ASSOCIATED WITH CHAINS L, H, W, AND/OR X. SOLVENT ...HETEROGEN SOLVENT ATOMS NUMBERED 1 - 125 ARE ASSOCIATED WITH CHAINS L, H, W, AND/OR X. SOLVENT ATOMS NUMBERED 601 - 749 ARE WITH CHAINS M, I, Y AND/OR Z. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pg7.cif.gz | 336.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pg7.ent.gz | 270.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/1pg7 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/1pg7 | 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: 23139.779 Da / Num. of mol.: 2 / Fragment: antigen-binding fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: GenBank: 15216020, UniProt: P01857*PLUS #2: Antibody | Mass: 23419.965 Da / Num. of mol.: 2 / Fragment: antigen-binding fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: GenBank: 15216022, UniProt: Q7Z3Y4*PLUS #3: Antibody | Mass: 22481.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: G0YP42*PLUS #4: Antibody | Mass: 23815.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863*PLUS #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: 2.89 Å3/Da / Density % sol: 57.49 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.917 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 21, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 72248 / Num. obs: 72248 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.477 / Num. unique all: 7157 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 310288 |
Reflection shell | *PLUS % possible obs: 98 % / Num. unique obs: 7157 / Num. measured obs: 26775 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1JPS, 1GIG Resolution: 2.5→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 34.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 2193 / % reflection Rfree: 3 % / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.219 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.411 / Rfactor Rwork: 0.341 |