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Yorodumi- PDB-3b5g: Crystal Structure of the Unstable and Highly Fibrillogenic PRO7SE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b5g | ||||||
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Title | Crystal Structure of the Unstable and Highly Fibrillogenic PRO7SER Mutant of the Recombinant Variable Domain 6AJL2 | ||||||
Components | AMYLOID LAMBDA 6 LIGHT CHAIN VARIABLE REGION PIP | ||||||
Keywords | IMMUNE SYSTEM / Lambda VI subgroup / light chain variable domain / beta-sandwich / immunoglobulin / AL amyloidosis | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hernandez-Santoyo, A. / Rodriguez-Romero, A. | ||||||
Citation | 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 | 3b5g.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b5g.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 3b5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b5g_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 3b5g_full_validation.pdf.gz | 464 KB | Display | |
Data in XML | 3b5g_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3b5g_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/3b5g ftp://data.pdbj.org/pub/pdb/validation_reports/b5/3b5g | HTTPS FTP |
-Related structure data
Related structure data | 2w0kC 3bdxC 2cd0S 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: 11951.873 Da / Num. of mol.: 2 / Fragment: residues 1-111 / Mutation: P7S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: Lambda VI light chain subgroup / Gene: VL gene segment 6a and JL2/3 gene segment / Plasmid: pSyn1 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Sequence details | THE RESIDUES ARE NUMBERED CONSECUTIV | |
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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: 2.45 Å3/Da / Density % sol: 49.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Drops consisted of 5 microL of protein solution (7 mg/mL) plus 5 microL of Solution 7 from Crystal Screen I (Hampton Research), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→53 Å / Num. all: 19189 / Num. obs: 19208 / % possible obs: 99.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.9→1.949 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1228 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2CD0 Resolution: 1.9→32.34 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.648 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.141 / 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: 19.235 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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