+Open data
-Basic information
Entry | Database: PDB / ID: 5mud | ||||||
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Title | Crystal structure of an amyloidogenic light chain dimer H6 | ||||||
Components | light chain dimer,IGL@ protein | ||||||
Keywords | IMMUNE SYSTEM / light chain dimer / light chain amyloidosis / immunoglobulin fold / protein aggregation | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Oberti, L. / Bacarizo, J. / Maritan, M. / Rognoni, P. / Bolognesi, M. / Ricagno, S. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Concurrent structural and biophysical traits link with immunoglobulin light chains amyloid propensity. Authors: Oberti, L. / Rognoni, P. / Barbiroli, A. / Lavatelli, F. / Russo, R. / Maritan, M. / Palladini, G. / Bolognesi, M. / Merlini, G. / Ricagno, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mud.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mud.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/5mud ftp://data.pdbj.org/pub/pdb/validation_reports/mu/5mud | HTTPS FTP |
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-Related structure data
Related structure data | 5m6aC 5m6iSC 5m76C 5mtlC 5muhC 5mvgC 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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Unit cell |
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-Components
#1: Antibody | Mass: 22763.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #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: 2.62 Å3/Da / Density % sol: 53.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bicine pH 9.0, 2% w/v 1,4-Dioxane, 10% w/v PEG 20K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97895 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→52.98 Å / Num. obs: 19281 / % possible obs: 96 % / Redundancy: 3.3 % / Biso Wilson estimate: 58.48 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.34→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.512 / Num. unique obs: 1908 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M6I Resolution: 2.34→52.98 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.313 / SU Rfree Blow DPI: 0.23 / SU Rfree Cruickshank DPI: 0.239
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Displacement parameters | Biso mean: 59.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.34→52.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.34→2.47 Å / Total num. of bins used: 10
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