+Open data
-Basic information
Entry | Database: PDB / ID: 3cdf | ||||||
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Title | kI O18/O8 Y87H immunoglobulin light chain variable domain | ||||||
Components | IMMUNOGLOBULIN LIGHT CHAIN | ||||||
Keywords | IMMUNE SYSTEM / Greek key beta barrel / amyloid / immunoglobulin / light chain / variable domain | ||||||
Function / homology | Function and homology information CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / 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 / 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 region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Baden, E.M. / Randles, E.G. / Thompson, J.R. / Ramirez-Alvarado, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural insights into the role of mutations in amyloidogenesis. Authors: Baden, E.M. / Randles, E.G. / Aboagye, A.K. / Thompson, J.R. / Ramirez-Alvarado, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cdf.cif.gz | 316.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cdf.ent.gz | 259.8 KB | Display | PDB format |
PDBx/mmJSON format | 3cdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/3cdf ftp://data.pdbj.org/pub/pdb/validation_reports/cd/3cdf | HTTPS FTP |
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-Related structure data
Related structure data | 3cdcC 3cdyC 2q20S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Antibody | Mass: 11946.093 Da / Num. of mol.: 6 / Mutation: Y87H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: kI O18/O8 germline / Plasmid: pET12a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P01594*PLUS #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE (UNIPROT) AT THE TIME OF ...THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE (UNIPROT) AT THE TIME OF DEPOSITION | |
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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: 3.18 Å3/Da / Density % sol: 61.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 1.2 M sodium citrate in 0.1 M Tris buffer, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5241 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 11, 2007 / Details: Osmic Varimax |
Radiation | Monochromator: confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5241 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→34.52 Å / Num. all: 177610 / Num. obs: 130900 / % possible obs: 73.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.31 % / Rsym value: 0.043 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.39→1.44 Å / Redundancy: 1.82 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.325 / % possible all: 13.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q20 Resolution: 1.53→17.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→17.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 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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