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- PDB-5gkr: Crystal structure of SLE patient-derived anti-DNA antibody in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gkr | ||||||
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Title | Crystal structure of SLE patient-derived anti-DNA antibody in complex with oligonucleotide | ||||||
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![]() | IMMUNE SYSTEM/DNA / antibody / lupus / DNA / Fab / IMMUNE SYSTEM-DNA complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DNA![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arimori, T. / Sakakibara, S. / Kikutani, H. / Takagi, J. | ||||||
![]() | ![]() Title: Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus Authors: Sakakibara, S. / Arimori, T. / Yamashita, K. / Jinzai, H. / Motooka, D. / Nakamura, S. / Li, S. / Takeda, K. / Katayama, J. / El Hussien, M.A. / Narazaki, M. / Tanaka, T. / Standley, D.M. / ...Authors: Sakakibara, S. / Arimori, T. / Yamashita, K. / Jinzai, H. / Motooka, D. / Nakamura, S. / Li, S. / Takeda, K. / Katayama, J. / El Hussien, M.A. / Narazaki, M. / Tanaka, T. / Standley, D.M. / Takagi, J. / Kikutani, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.7 KB | Display | ![]() |
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PDB format | ![]() | 263.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 449.6 KB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 42.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gksC ![]() 4idjS ![]() 4llwS ![]() 4qhkS ![]() 4y5yS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Antibody | Mass: 23397.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 22948.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: DNA chain | | Mass: 1171.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl (pH 7.0), 0.2 M NaCl, 1 M Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 9, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 53509 / % possible obs: 100 % / Redundancy: 5.8 % / Rsym value: 0.115 / Net I/σ(I): 23.1 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.857 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QHK, 4Y5Y, 4IDJ, and 4LLW Resolution: 2.1→26.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.593 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.03 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.752 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→26.33 Å
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Refine LS restraints |
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