+Open data
-Basic information
Entry | Database: PDB / ID: 3o11 | |||||||||
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Title | Anti-beta-amyloid antibody c706 fab in space group c2 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin fold | |||||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / Fc epsilon receptor (FCERI) signaling / 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 / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / Potential therapeutics for SARS / adaptive immune response / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. | |||||||||
Citation | Journal: J.Mol.Recognit. / Year: 2011 Title: His-tag binding by antibody C706 mimics beta-amyloid recognition. Authors: Teplyakov, A. / Obmolova, G. / Canziani, G. / Zhao, Y. / Gutshall, L. / Jung, S.S. / Gilliland, G.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o11.cif.gz | 176.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o11.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 3o11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/3o11 ftp://data.pdbj.org/pub/pdb/validation_reports/o1/3o11 | HTTPS FTP |
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-Related structure data
Related structure data | 3mclSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 23057.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: IGKC / Cell (production host): HUMAN EMBRYONIC KIDNEY (HEK) CELLS / Production host: HOMO SAPIENS (human) / References: UniProt: P01834 #2: Antibody | Mass: 24200.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: IGHG1 / Cell (production host): HUMAN EMBRYONIC KIDNEY (HEK) CELLS / Production host: HOMO SAPIENS (human) / References: UniProt: P01857 #3: 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: 2.56 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / pH: 3.5 Details: 0.1 M CITRATE PH 3.5, 18% PEG 8000 CRYO CONDITIONS, 0.1 M CITRATE PH 3.5, 25% PEG 8000, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 26, 2008 / Details: VARIMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→53 Å / Num. obs: 20634 / % possible obs: 85.4 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 96 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.4 / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MCL Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.886 / SU B: 22.849 / SU ML: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.543 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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