+Open data
-Basic information
Entry | Database: PDB / ID: 3mcl | |||||||||
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Title | Anti-beta-amyloid antibody c706 fab in space group P21 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / MONOCLONAL ANTIBODY | |||||||||
Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / antigen binding / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / 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: 1.7 Å | |||||||||
Authors | Teplyakov, A. / Obmolova, G. / Gilliland, G.L. | |||||||||
Citation | Journal: J.Mol.Recognit. / Year: 2010 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 | 3mcl.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mcl.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/3mcl ftp://data.pdbj.org/pub/pdb/validation_reports/mc/3mcl | HTTPS FTP |
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-Related structure data
Related structure data | 3o11C 1eo8S 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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Unit cell |
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-Components
#1: Antibody | Mass: 23074.598 Da / Num. of mol.: 1 Fragment: CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens Cell (production host): Human embryonic kidney (HEK) 293 cells Production host: Homo Sapiens (human) |
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#2: Antibody | Mass: 24200.965 Da / Num. of mol.: 1 Fragment: FD fragment of the heavy chain, CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens Cell (production host): Human embryonic kidney (HEK) 293 cells Production host: Homo sapiens (human) / References: UniProt: P01857*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: 2.06 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 3350, 0.2 M SODIUM THIOCYANATE; CRYO CONDITIONS: 0.1 M HEPES PH 7.0, 24% PEG 3350, 0.2 M SODIUM THIOCYANATE, 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 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 27, 2008 / Details: VARIMAX HF |
Radiation | Monochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→69 Å / Num. all: 42232 / Num. obs: 42232 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.3 / % possible all: 85.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EO8 Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.607 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.136 / 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: 36.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.134 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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