+Open data
-Basic information
Entry | Database: PDB / ID: 5mtl | ||||||
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Title | Crystal structure of an amyloidogenic light chain | ||||||
Components | light chain dimer,IGL@ protein,IGL@ protein | ||||||
Keywords | IMMUNE SYSTEM / light chain dimer / light chain amyloidosis / immunoglobulin fold / protein aggregation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 | 5mtl.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mtl.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mtl_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 5mtl_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 5mtl_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 5mtl_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/5mtl ftp://data.pdbj.org/pub/pdb/validation_reports/mt/5mtl | HTTPS FTP |
-Related structure data
Related structure data | 5m6aC 5m6iSC 5m76C 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 22756.051 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Production host: Escherichia coli (E. coli) / References: UniProt: Q567P1 #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: 2.88 Å3/Da / Density % sol: 57.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium cacodylate, 27% w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 126.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→28.57 Å / Num. obs: 36581 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3606 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M6I Resolution: 2.45→29.289 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→29.289 Å
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Refine LS restraints |
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LS refinement shell |
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