+Open data
-Basic information
Entry | Database: PDB / ID: 1qp1 | ||||||
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Title | KAPPA VARIABLE LIGHT CHAIN | ||||||
Components | BENCE-JONES KAPPA I ANTIBODY BRE (LIGHT CHAIN) | ||||||
Keywords | IMMUNE SYSTEM / BETA SANDWICH / DOUBLE SPIRAL | ||||||
Function / homology | Function and homology information CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / 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 / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / 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 / antigen binding / Regulation of Complement cascade / 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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Steinrauf, L.K. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 1999 Title: Molecular structure of the amyloid-forming protein kappa I Bre. Authors: Steinrauf, L.K. / Chiang, M.Y. / Shiuan, D. #1: Journal: Am.Cryst.Assoc.,Abstr.Papers (Annual Meeting) / Year: 1993 Title: Structure of an Immunoglubulin Kappa Variable Light Chain Associated with Primary Amyloidosis Authors: Steinrauf, L.K. / Hamilton, J.A. / Clawson, D. / Liepnieks, J. / Murrell, J. / Benson, M.D. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: Tertiary Structure of an Amyloid Immunoglobulin Light Chain Protein: A Proposed Model for Amyloid Fibril Formation Authors: Schormann, N. / Murrell, J.R. / Liepnieks, J.R. / Benson, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qp1.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qp1.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/1qp1 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/1qp1 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 11787.930 Da / Num. of mol.: 3 / Fragment: IMMUNOGLOBULIN FRAGMENT, VARIABLE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BONE MARROW / Plasmid: PCZ11 / Production host: Escherichia coli (E. coli) / References: PIR: I39154, UniProt: P01594*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: 3.26 Å3/Da / Density % sol: 62.24 % | ||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: AMMONIUM SULFATE, CITRATE BUFFER, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 11, 1992 |
Radiation | Monochromator: BENT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→60 Å / Num. all: 89999 / Num. obs: 22485 / % possible obs: 68.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.06→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 1.92 / % possible all: 50.25 |
Reflection shell | *PLUS % possible obs: 50.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THE BENCE-JONES PROTEINS ROY: COLMAN, SCHRAMM, GURS J. MOL. BIOL. 116, 73, 1977 AND REI: EPP, COLMAN, FEHLHAMMER, BODE, SCHIFFER, HUBER, AND PALM EUR. J. BIOCHEM. 45, 513 1974 Resolution: 2.06→20 Å / Num. parameters: 1040 / Num. restraintsaints: 984 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2708 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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