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Yorodumi- PDB-1nbv: AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nbv | ||||||
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Title | AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX | ||||||
Components |
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Keywords | IMMUNOGLOBULIN | ||||||
Function / homology | Function and homology information Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / immune response / extracellular space / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Herron, J.N. / He, X.M. / Edmundson, A.B. | ||||||
Citation | Journal: Proteins / Year: 1991 Title: An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex. Authors: Herron, J.N. / He, X.M. / Ballard, D.W. / Blier, P.R. / Pace, P.E. / Bothwell, A.L. / Voss Jr., E.W. / Edmundson, A.B. #1: Journal: Mol.Immunol. / Year: 1985 Title: Crystallographic Characterization of the Fab Fragment of a Monoclonal Anti-Ss-DNA Antibody Authors: Gibson, A.L. / Herron, J.N. / Ballard, D.W. / Voss, E.W. / He, X.M. / Patrick, V.A. / Edmundson, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nbv.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nbv.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 1nbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nbv_validation.pdf.gz | 378.9 KB | Display | wwPDB validaton report |
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Full document | 1nbv_full_validation.pdf.gz | 410.3 KB | Display | |
Data in XML | 1nbv_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 1nbv_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/1nbv ftp://data.pdbj.org/pub/pdb/validation_reports/nb/1nbv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO L 8, PRO L 100, PRO L 146, PRO H 155, AND PRO H 197 ARE CIS PROLINES. |
-Components
#1: Antibody | Mass: 24109.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: PIR: S16112, UniProt: A2NHM3*PLUS |
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#2: Antibody | Mass: 23553.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01867 |
Sequence details | THE PROTEIN WAS SEQUENCED BY D.W. BALLARD, P.R. BLIER, P.E. PACE, AND A.L.M. BOTHWELL, REFERENCE 1 ABOVE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.6 / Method: unknown |
Components of the solutions | *PLUS Conc.: 1.7 M / Common name: ammonium sulfate |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 19716 / % possible obs: 72 % / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Resolution: 2→6 Å /
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 18797 / Rfactor obs: 0.246 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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