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Yorodumi- PDB-1dcl: MCG, A LAMBDA V TYPE LIGHT-CHAIN DIMER (BENCE-JONES PROTEIN), CRY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dcl | ||||||
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Title | MCG, A LAMBDA V TYPE LIGHT-CHAIN DIMER (BENCE-JONES PROTEIN), CRYSTALLIZED FROM AMMONIUM SULFATE | ||||||
Components | MCG | ||||||
Keywords | IMMUNOGLOBULIN / BENCE JONES / ANTIBODY / MULTIPLE QUATERNARY STRUCTURES | ||||||
Function / homology | Function and homology information 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 / antigen binding / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Schiffer, M. / Xu, Z.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1989 Title: Three-dimensional structure of a light chain dimer crystallized in water. Conformational flexibility of a molecule in two crystal forms. Authors: Ely, K.R. / Herron, J.N. / Harker, M. / Edmundson, A.B. #1: Journal: Am.Cryst.Assoc.,Abstr.Papers (Annual Meeting) / Year: 1988 Title: The Refinement and Structure of Mcg Bence-Jones Dimer at 2.3 Angstroms Resolution Authors: Xu, Z.B. / Schiffer, M. #2: Journal: Biochemistry / Year: 1973 Title: Structure of a Lambda-Type Bence-Jones Protein at 3.5-A Resolution Authors: Schiffer, M. / Girling, R.L. / Ely, K.R. / Edmundson, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dcl.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dcl.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dcl_validation.pdf.gz | 428.5 KB | Display | wwPDB validaton report |
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Full document | 1dcl_full_validation.pdf.gz | 464.8 KB | Display | |
Data in XML | 1dcl_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 1dcl_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/1dcl ftp://data.pdbj.org/pub/pdb/validation_reports/dc/1dcl | HTTPS FTP |
-Related 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: 22818.096 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: A LAMBDA V TYPE LIGHT-CHAIN DIMER / Source: (natural) Homo sapiens (human) / References: UniProt: P01709 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.95 % | ||||||||||||||||||
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Crystal grow | Details: CRYSTALLIZED FROM AMMONIUM SULFATE | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: microdialysis / Details: Abola, E.E., (1980) Biochemistry, 19, 432. | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.14 / Highest resolution: 2.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.3 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.14 / Rfactor Rwork: 0.14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |