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Open data
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Basic information
Entry | Database: PDB / ID: 5od0 | |||||||||
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Title | Crystal structure of ACPA E4 | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dobritzsch, D. / Ge, C. / Holmdahl, R. | |||||||||
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 | ![]() | 187.7 KB | Display | ![]() |
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PDB format | ![]() | 148.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ockC ![]() 5ocxSC ![]() 5ocyC ![]() 5od8C ![]() 5odbC 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
#1: Antibody | Mass: 23261.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: B cell clone of a rheumatoid arthritis patient / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Antibody | Mass: 23340.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: B cell clone of a rheumatoid arthritis patient / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-GOL / ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 37.8 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20% (w/v) PEG 6000, 0.1 M MES pH 6.0, 0.2 M ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→34.3 Å / Num. obs: 40031 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.0215 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.8→1.864 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 8 / Num. unique obs: 3926 / CC1/2: 0.975 / Rpim(I) all: 0.091 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5OCX (early model) Resolution: 1.8→34.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.813 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / 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: 21.041 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→34.3 Å
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Refine LS restraints |
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