[English] 日本語
Yorodumi- PDB-1uus: Structure of an activated Dictyostelium STAT in its DNA-unbound form -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uus | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of an activated Dictyostelium STAT in its DNA-unbound form | ||||||
Components | STAT PROTEIN | ||||||
Keywords | SIGNAL TRANSDUCTION / DICTYOSTELIUM / STAT / SH2 / TRANSDUCER / TRANSCRIPTION FACTOR | ||||||
Function / homology | Function and homology information Interleukin-6 signaling / Signaling by ALK / STAT6-mediated induction of chemokines / Interleukin-10 signaling / Interleukin-4 and Interleukin-13 signaling / Interferon gamma signaling / Interleukin-20 family signaling / Interleukin-15 signaling / Interleukin-35 Signalling / Interleukin-9 signaling ...Interleukin-6 signaling / Signaling by ALK / STAT6-mediated induction of chemokines / Interleukin-10 signaling / Interleukin-4 and Interleukin-13 signaling / Interferon gamma signaling / Interleukin-20 family signaling / Interleukin-15 signaling / Interleukin-35 Signalling / Interleukin-9 signaling / Interleukin-37 signaling / Interleukin-12 signaling / Interleukin-23 signaling / Interleukin-27 signaling / Interferon alpha/beta signaling / STAT3 nuclear events downstream of ALK signaling / sorocarp stalk cell differentiation / ISG15 antiviral mechanism / sorocarp development / cell surface receptor signaling pathway via STAT / culmination involved in sorocarp development / cell surface receptor signaling pathway via JAK-STAT / defense response / regulation of gene expression / regulation of cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of gene expression / DNA binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å | ||||||
Authors | Soler-Lopez, M. / Petosa, C. / Fukuzawa, M. / Ravelli, R. / Williams, J.G. / Muller, C.W. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Structure of an Activated Dictyostelium Stat in its DNA-Unbound Form Authors: Soler-Lopez, M. / Petosa, C. / Fukuzawa, M. / Ravelli, R. / Williams, J.G. / Muller, C.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1uus.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1uus.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 1uus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uus_validation.pdf.gz | 433 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1uus_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 1uus_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 1uus_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/1uus ftp://data.pdbj.org/pub/pdb/validation_reports/uu/1uus | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53376.727 Da / Num. of mol.: 1 / Fragment: RESIDUES 235-707 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TKB1 / References: UniProt: O00910 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.836 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: 1 M NaCl, 150 mM ammonium acetate, 5 mM MgSO4, 50 mM MES pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.072 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 15362 / % possible obs: 99.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 100 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 2.8→50 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2199841 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 355-358 WERE MODELED AS POLYGLYCINE. RESIDUES 415-418 WERE OMITTED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.194 Å2 / ksol: 0.31917 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|