[English] 日本語
Yorodumi- PDB-6d4n: Crystal structure of a Fc fragment of Rhesus macaque (Macaca mula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d4n | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a Fc fragment of Rhesus macaque (Macaca mulatta) IgG4 | |||||||||
Components | Fc fragment of IgG4 | |||||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / IGG4 / IMMUNOGLOBULIN-LIKE BETA SANDWICH / FC FRAGMENT | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Macaca mulatta (Rhesus monkey) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | |||||||||
Authors | Gohain, N. / Tolbert, W.D. / Pazgier, M. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: Mabs / Year: 2019 Title: From Rhesus macaque to human: structural evolutionary pathways for immunoglobulin G subclasses. Authors: Tolbert, W.D. / Subedi, G.P. / Gohain, N. / Lewis, G.K. / Patel, K.R. / Barb, A.W. / Pazgier, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6d4n.cif.gz | 191 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6d4n.ent.gz | 153.2 KB | Display | PDB format |
PDBx/mmJSON format | 6d4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/6d4n ftp://data.pdbj.org/pub/pdb/validation_reports/d4/6d4n | HTTPS FTP |
---|
-Related structure data
Related structure data | 6d4eC 6d4iC 6d4mC 4c54S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25066.355 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.81 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.34% PEG 8000 335 ammonium citrate pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2015 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→50 Å / Num. obs: 7018 / % possible obs: 98.9 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.044 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 3.25→3.3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.65 / Rpim(I) all: 0.491 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C54 Resolution: 3.25→35.634 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.76 / Phase error: 33.89
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→35.634 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|