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- PDB-1pew: High Resolution Crystal Structure of Jto2, a mutant of the non-am... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pew | ||||||
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Title | High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto | ||||||
![]() | Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN | ||||||
![]() | IMMUNE SYSTEM / Beta Sheet | ||||||
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 / immune response / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dealwis, C. / Gupta, V. / Wilkerson, M. | ||||||
![]() | ![]() Title: Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four V(lambda)6 proteins Authors: Wall, J.S. / Gupta, V. / Wilkerson, M. / Schell, M. / Loris, R. / Adams, P. / Solomon, A. / Stevens, F. / Dealwis, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.2 KB | Display | ![]() |
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PDB format | ![]() | 42.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.4 KB | Display | ![]() |
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Full document | ![]() | 445.3 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pw3C ![]() 1cd0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 11898.972 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN / Mutation: D29A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M Na Acetate, 0.8M Amm. Sulfate, 100mM Cadmium chloride, 10% n-Decyl-B-D-maltoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Sep 15, 2001 |
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: 1.6→15 Å / Num. all: 32368 / Num. obs: 31495 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Rsym value: 0.066 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 3339 / Rsym value: 0.515 / % possible all: 93.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CD0 Resolution: 1.6→8 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.385 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.125 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.751 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 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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