+Open data
-Basic information
Entry | Database: PDB / ID: 2ask | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human Artemin | ||||||
Components | artemin | ||||||
Keywords | HORMONE/GROWTH FACTOR / Glial cell derived family ligand / neurotrphoic growth factor / sulfates / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information glial cell-derived neurotrophic factor receptor binding / Peyer's patch morphogenesis / lymphocyte migration into lymphoid organs / induction of positive chemotaxis / peripheral nervous system development / NCAM1 interactions / neuroblast proliferation / RET signaling / axon guidance / growth factor activity ...glial cell-derived neurotrophic factor receptor binding / Peyer's patch morphogenesis / lymphocyte migration into lymphoid organs / induction of positive chemotaxis / peripheral nervous system development / NCAM1 interactions / neuroblast proliferation / RET signaling / axon guidance / growth factor activity / receptor tyrosine kinase binding / RAF/MAP kinase cascade / signaling receptor binding / signal transduction / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.55 Å | ||||||
Authors | Silvian, L. / Jin, P. / Carmillo, P. / Boriack-Sjodin, P.A. / Pelletier, C. / Rushe, M. / Gong, B.J. / Sah, D. / Pepinsky, B. / Rossomando, A. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Artemin crystal structure reveals insights into heparan sulfate binding. Authors: Silvian, L. / Jin, P. / Carmillo, P. / Boriack-Sjodin, P.A. / Pelletier, C. / Rushe, M. / Gong, B.J. / Sah, D. / Pepinsky, B. / Rossomando, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ask.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ask.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ask.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/2ask ftp://data.pdbj.org/pub/pdb/validation_reports/as/2ask | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11984.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: GenBank: 55959167, UniProt: Q5T4W7*PLUS #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.31 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Magnesium Sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 2001 | ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. all: 30142 / Num. obs: 29225 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 19.3 | ||||||||||||||||||
Reflection shell | Highest resolution: 1.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2719 / Rsym value: 0.31 / % possible all: 95.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.55→15.6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 483024.53 / Data cutoff high rms absF: 483024.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.8269 Å2 / ksol: 0.425408 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→15.6 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|