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Yorodumi- PDB-5c9k: Crystal structure of a highly fibrillogenic Arg24Gly mutant of th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c9k | ||||||
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Title | Crystal structure of a highly fibrillogenic Arg24Gly mutant of the Recombinant variable domain 6AJL2 | ||||||
Components | Amyloid lambda 6 light chain variable region PIP | ||||||
Keywords | IMMUNE SYSTEM / LAMBDA VI SUBGROUP / BETA-SANDWICH / IMMUNOGLOBULIN / AL AMYLOIDOSIS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Hernandez-Santoyo, A. / Rodriguez-Romero, A. / Luna-Martinez, O.D. / Becerril-Lujan, B. | ||||||
Citation | Journal: To Be Published Title: Mutating amyloidogenic lambda6 light chain AR back to germline 6aJL2 Authors: Luna-Martinez, O.D. / Villalba-Velazquez, M.I. / Sanchez-Alcala, R. / Hernandez-Santoyo, A. / Fernandez-Velasco, D.A. / Rodriguez-Romero, A. / Becerril-Lujan, B. #1: Journal: J. Mol. Biol. / Year: 2010 Title: A single mutation at the sheet switch region results in conformational changes favoring lambda6 light-chain fibrillogenesis. Authors: Hernandez-Santoyo, A. / del Pozo Yauner, L. / Fuentes-Silva, D. / Ortiz, E. / Rudino-Pinera, E. / Sanchez-Lopez, R. / Horjales, E. / Becerril, B. / Rodriguez-Romero, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c9k.cif.gz | 199.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c9k.ent.gz | 158.3 KB | Display | PDB format |
PDBx/mmJSON format | 5c9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c9k_validation.pdf.gz | 477.1 KB | Display | wwPDB validaton report |
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Full document | 5c9k_full_validation.pdf.gz | 477.9 KB | Display | |
Data in XML | 5c9k_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 5c9k_validation.cif.gz | 64.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/5c9k ftp://data.pdbj.org/pub/pdb/validation_reports/c9/5c9k | HTTPS FTP |
-Related structure data
Related structure data | 3b5gS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 11861.768 Da / Num. of mol.: 8 / Mutation: R24G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VL GENE SEGMENT 6A AND JL2/3 GENE SEGMENT / Plasmid: PSYN1 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 / References: UniProt: Q96JD1*PLUS #2: Chemical | ChemComp-ACT / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: SOLUTION 7 FROM CRYSTAL REMARK 280 SCREEN I (HAMPTON RESEARCH), PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→34.7 Å / Num. all: 76561 / Num. obs: 76561 / % possible obs: 100 % / Redundancy: 2.9 % / Biso Wilson estimate: 19.56 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.92→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B5G Resolution: 1.92→34.646 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→34.646 Å
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Refine LS restraints |
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LS refinement shell |
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