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Open data
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Basic information
Entry | Database: PDB / ID: 1i1c | |||||||||
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Title | NON-FCRN BINDING FC FRAGMENT OF RAT IGG2A | |||||||||
![]() | IG GAMMA-2A CHAIN C REGION | |||||||||
![]() | IMMUNE SYSTEM / igg / fc | |||||||||
Function / homology | ![]() immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Martin, W.L. / West Jr., A.P. / Gan, L. / Bjorkman, P.J. | |||||||||
![]() | ![]() Title: Crystal structure at 2.8 A of an FcRn/heterodimeric Fc complex: mechanism of pH-dependent binding. Authors: Martin, W.L. / West Jr., A.P. / Gan, L. / Bjorkman, P.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 76.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i1aC ![]() 1fc1S 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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1 |
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Unit cell |
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Details | The biological unit is the glycosylated homodimer |
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Components
#1: Protein | Mass: 26650.855 Da / Num. of mol.: 2 / Fragment: FC FRAGMENT / Mutation: T252G, I253G, T254G, H310E, H433E, H435E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.48 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 4000 ammonium acetate tri-sodium acetate dihydrate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 2, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 13471 / Num. obs: 13471 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.056 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 1 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1323 / Rsym value: 0.261 / % possible all: 87.2 |
Reflection | *PLUS Num. obs: 14919 / % possible obs: 97.5 % / Num. measured all: 35621 |
Reflection shell | *PLUS % possible obs: 87.2 % / Num. unique obs: 1323 / Num. measured obs: 3003 / Rmerge(I) obs: 0.261 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1fc1 Resolution: 2.7→29.81 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1496783.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.8197 Å2 / ksol: 0.328263 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.81 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10.2 % / Rfactor obs: 0.241 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.404 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.325 |