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Yorodumi- PDB-5m6i: Crystal structure of non-cardiotoxic Bence-Jones light chain dimer M8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m6i | |||||||||
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Title | Crystal structure of non-cardiotoxic Bence-Jones light chain dimer M8 | |||||||||
Components | (light chain dimer) x 2 | |||||||||
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: 2.2 Å | |||||||||
Authors | Oberti, L. / Rognoni, P. / Russo, R. / Bacarizo, J. / 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 | 5m6i.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m6i.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/5m6i ftp://data.pdbj.org/pub/pdb/validation_reports/m6/5m6i | HTTPS FTP |
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-Related structure data
Related structure data | 5m6aSC 5m76C 5mtlC 5mudC 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 22863.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Urine | ||
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#2: Antibody | Mass: 22846.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Urine | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.2 M Sodium acetate, 2.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→57.34 Å / Num. obs: 43679 / % possible obs: 99.7 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.271 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 14.6 % / Rmerge(I) obs: 2.548 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M6A Resolution: 2.2→54.56 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→54.56 Å
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Refine LS restraints |
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LS refinement shell |
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