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Open data
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Basic information
Entry | Database: PDB / ID: 5od8 | |||||||||
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Title | Crystal structure of the RA-associated mAb B2 (Fab fragment) | |||||||||
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![]() | IMMUNE SYSTEM / antibody Fab fragment / IMMUNE SYSTEM rheumatoid arthritis associated | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dobritzsch, D. / Ge, C. / Holmdahl, R. / Amara, K. / Malmstrom, V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Cross-Reactivity of Anti-Citrullinated Protein Antibodies. Authors: Ge, C. / Xu, B. / Liang, B. / Lonnblom, E. / Lundstrom, S.L. / Zubarev, R.A. / Ayoglu, B. / Nilsson, P. / Skogh, T. / Kastbom, A. / Malmstrom, V. / Klareskog, L. / Toes, R.E.M. / Rispens, T. ...Authors: Ge, C. / Xu, B. / Liang, B. / Lonnblom, E. / Lundstrom, S.L. / Zubarev, R.A. / Ayoglu, B. / Nilsson, P. / Skogh, T. / Kastbom, A. / Malmstrom, V. / Klareskog, L. / Toes, R.E.M. / Rispens, T. / Dobritzsch, D. / Holmdahl, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.5 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.4 KB | Display | ![]() |
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Full document | ![]() | 426.1 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ockC ![]() 5ocxC ![]() 5ocyC ![]() 5od0C ![]() 5odbC ![]() 3ncjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 24275.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell line (production host): 293 embryonic kidney fibroblasts Production host: ![]() |
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#2: Antibody | Mass: 23236.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell line (production host): 293 embryonic kidney fibroblasts Production host: ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 53.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG3350, 0.2 M Na3citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→92.53 Å / Num. obs: 25795 / % possible obs: 94.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.051 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3 / Num. unique obs: 1602 / CC1/2: 0.791 / Rpim(I) all: 0.243 / % possible all: 69.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ncj Resolution: 2.2→92.52 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.837 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.211 / 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: 42.519 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→92.52 Å
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Refine LS restraints |
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