+Open data
-Basic information
Entry | Database: PDB / ID: 1kcu | ||||||
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Title | CRYSTAL STRUCTURE OF ANTIBODY PC287 | ||||||
Components | (PC287 IMMUNOGLOBULIN) x 2 | ||||||
Keywords | IMMUNE SYSTEM / ANTI-PEPTIDE ANTIBODY | ||||||
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 / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / IgG immunoglobulin complex / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nair, D.T. / Singh, K. / Siddiqui, Z. / Nayak, B.P. / Rao, K.V.S. / Salunke, D.M. | ||||||
Citation | Journal: J.Immunol. / Year: 2002 Title: Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response. Authors: Nair, D.T. / Singh, K. / Siddiqui, Z. / Nayak, B.P. / Rao, K.V. / Salunke, D.M. #1: Journal: J.IMMUNOL. / Year: 2000 Title: Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-antibody Recognition Authors: Nair, D.T. / Singh, K. / Sahu, N. / Rao, K.V. / Salunke, D.M. | ||||||
History |
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Remark 999 | SEQUENCE An appropriate sequence database match for the Immunoglobulin was not available at the ...SEQUENCE An appropriate sequence database match for the Immunoglobulin was not available at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kcu.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kcu.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kcu ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kcu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23478.830 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837 |
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#2: Antibody | Mass: 23205.986 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1A4, UniProt: P01869*PLUS |
#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: 2.46 Å3/Da / Density % sol: 49.91 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 15% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 19589 / % possible obs: 85 % / Redundancy: 8 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 14215 / % possible obs: 85 % / Num. measured all: 157194 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 81.8 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 148770.82 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.8358 Å2 / ksol: 0.305654 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 403 / Rfactor Rwork: 0.381 / Rfactor obs: 0.381 |