+Open data
-Basic information
Entry | Database: PDB / ID: 5gw9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of C163, a backbone circularized G-CSF | ||||||
Components | Granulocyte colony-stimulating factor | ||||||
Keywords | CYTOKINE / four-helix bundle / backbone circulatization | ||||||
Function / homology | Function and homology information granulocyte colony-stimulating factor receptor binding / granulocyte colony-stimulating factor signaling pathway / positive regulation of myeloid cell differentiation / granulocyte differentiation / regulation of actin filament organization / Other interleukin signaling / positive regulation of actin filament polymerization / cellular response to cytokine stimulus / Interleukin-10 signaling / endocytic vesicle lumen ...granulocyte colony-stimulating factor receptor binding / granulocyte colony-stimulating factor signaling pathway / positive regulation of myeloid cell differentiation / granulocyte differentiation / regulation of actin filament organization / Other interleukin signaling / positive regulation of actin filament polymerization / cellular response to cytokine stimulus / Interleukin-10 signaling / endocytic vesicle lumen / Signaling by CSF3 (G-CSF) / lysosomal lumen / cytokine activity / growth factor activity / Inactivation of CSF3 (G-CSF) signaling / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / response to ethanol / cellular response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / immune response / positive regulation of cell population proliferation / enzyme binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Miyafusa, T. / Honda, S. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Structural insights into the backbone-circularized granulocyte colony-stimulating factor containing a short connector. Authors: Miyafusa, T. / Shibuya, R. / Honda, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5gw9.cif.gz | 279.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5gw9.ent.gz | 228.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/5gw9 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gw9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2d9qS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17596.252 Da / Num. of mol.: 4 / Fragment: UNP residues 40-202 / Mutation: P40S, C47S, A205G Source method: isolated from a genetically manipulated source Details: 1st Ser and 173rd Gly are connected with a peptide bond. Source: (gene. exp.) Homo sapiens (human) / Gene: CSF3, C17orf33, GCSF / Production host: Escherichia coli (E. coli) / References: UniProt: P09919 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.76 % |
---|---|
Crystal grow | Temperature: 293 K / Method: evaporation / Details: 0.4M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 89146 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 35.5 |
Reflection shell | Resolution: 1.65→1.693 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D9Q Resolution: 1.65→34.08 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.043 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.453 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.65→34.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|