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Yorodumi- PDB-1lil: BENCE JONES PROTEIN CLE, A LAMBDA III IMMUNOGLOBULIN LIGHT-CHAIN DIMER -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lil | ||||||
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Title | BENCE JONES PROTEIN CLE, A LAMBDA III IMMUNOGLOBULIN LIGHT-CHAIN DIMER | ||||||
Components | LAMBDA III BENCE JONES PROTEIN CLE | ||||||
Keywords | IMMUNOGLOBULIN / BENCE JONES PROTEIN | ||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / 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 / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / 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 / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Schiffer, M. / Huang, D.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Pitfalls of molecular replacement: the structure determination of an immunoglobulin light-chain dimer. Authors: Huang, D.B. / Ainsworth, C. / Solomon, A. / Schiffer, M. #1: Journal: J.Mol.Biol. / Year: 1981 Title: Preliminary Crystallographic Data on the Human Lambda III Bence Jones Protein Dimer Cle Authors: Stevens, F.J. / Westholm, F.A. / Panagiotopoulos, N. / Solomon, A. / Schiffer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lil.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lil.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/1lil ftp://data.pdbj.org/pub/pdb/validation_reports/li/1lil | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 22692.049 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01842, UniProt: P0DOY3*PLUS #2: 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: 2.16 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 1.8 M AMMONIUM SULFATE PH 7.0 | ||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis / Details: Stevens, F.J., (1981) J.Mol.Biol., 147, 179. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: 1989 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.65 Å / Num. obs: 11373 / % possible obs: 92 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.047 |
Reflection | *PLUS Lowest resolution: 10.5 Å / Num. measured all: 55038 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MCG(AS) Resolution: 2.65→10 Å / σ(F): 2 / Details: X-PLOR WAS USED IN THE EARLY STAGES OF REFINEMENT.
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Displacement parameters | Biso mean: 15.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |