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Yorodumi- PDB-1b0w: Structural comparison of amyloidogenic light chain dimer in two c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b0w | ||||||
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Title | Structural comparison of amyloidogenic light chain dimer in two crystal forms with nonamyloidogenic counterparts | ||||||
Components | BENCE-JONES KAPPA I PROTEIN BRE | ||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / AMYLOID | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Schormann, N. / Benson, M.D. | ||||||
Citation | Journal: Amyloid / Year: 1998 Title: Tertiary structures of amyloidogenic and non-amyloidogenic transthyretin variants: new model for amyloid fibril formation Authors: Schormann, N. / Murrell, J.R. / Benson, M.D. #1: 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.J. / 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 | 1b0w.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b0w.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b0w_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
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Full document | 1b0w_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 1b0w_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1b0w_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/1b0w ftp://data.pdbj.org/pub/pdb/validation_reports/b0/1b0w | HTTPS FTP |
-Related structure data
Related structure data | 1bzdC 1bzeC 1tshC 2trhC 2tryC 1breS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | monomer |
-Components
#1: Antibody | Mass: 11945.124 Da / Num. of mol.: 3 / Fragment: VARIABLE DOMAIN OF LIGHT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: PATIENT BRE / Plasmid: PCZ11 Gene (production host): CDNA (GENBANK ACCESSION CODE U31344) Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P01594 #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: 3.2 Å3/Da / Density % sol: 61.15 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: CRYSTALS OF BRE (20MG/ML IN 0.1M TRIS BUFFER, PH 7) WERE GROWN AT RT IN HANGING-DROPS USING 2.5M AMMONIUM SULFATE IN 0.1M CITRATE BUFFER (PH 5.5)., pH 6.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1994 / Details: COLLIMATOR |
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: 1.75→52.5 Å / Num. obs: 35142 / % possible obs: 76 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.047 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.75→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 1.92 / Rsym value: 0.255 / % possible all: 56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BRE Resolution: 1.8→5 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Xplor file |
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