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Open data
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Basic information
Entry | Database: PDB / ID: 3cdf | ||||||
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Title | kI O18/O8 Y87H immunoglobulin light chain variable domain | ||||||
![]() | IMMUNOGLOBULIN LIGHT CHAIN | ||||||
![]() | IMMUNE SYSTEM / Greek key beta barrel / amyloid / immunoglobulin / light chain / variable domain | ||||||
Function / homology | ![]() CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / 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 / antigen binding / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Baden, E.M. / Randles, E.G. / Thompson, J.R. / Ramirez-Alvarado, M. | ||||||
![]() | ![]() Title: Structural insights into the role of mutations in amyloidogenesis. Authors: Baden, E.M. / Randles, E.G. / Aboagye, A.K. / Thompson, J.R. / Ramirez-Alvarado, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.1 KB | Display | ![]() |
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PDB format | ![]() | 259.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.1 KB | Display | ![]() |
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Full document | ![]() | 431.9 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cdcC ![]() 3cdyC ![]() 2q20S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 11946.093 Da / Num. of mol.: 6 / Mutation: Y87H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE (UNIPROT) AT THE TIME OF ...THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE (UNIPROT) AT THE TIME OF DEPOSITION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 1.2 M sodium citrate in 0.1 M Tris buffer, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 11, 2007 / Details: Osmic Varimax |
Radiation | Monochromator: confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5241 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→34.52 Å / Num. all: 177610 / Num. obs: 130900 / % possible obs: 73.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.31 % / Rsym value: 0.043 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.39→1.44 Å / Redundancy: 1.82 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.325 / % possible all: 13.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2Q20 Resolution: 1.53→17.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→17.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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