+Open data
-Basic information
Entry | Database: PDB / ID: 4gfx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal domain of TXNIP | ||||||
Components | Thioredoxin-interacting protein | ||||||
Keywords | PROTEIN BINDING / Arrestin-like fold | ||||||
Function / homology | Function and homology information cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cell division / enzyme inhibitor activity / Regulation of FOXO transcriptional activity by acetylation / The NLRP3 inflammasome / platelet-derived growth factor receptor signaling pathway / response to glucose / Purinergic signaling in leishmaniasis infection / response to mechanical stimulus ...cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cell division / enzyme inhibitor activity / Regulation of FOXO transcriptional activity by acetylation / The NLRP3 inflammasome / platelet-derived growth factor receptor signaling pathway / response to glucose / Purinergic signaling in leishmaniasis infection / response to mechanical stimulus / keratinocyte differentiation / response to progesterone / response to hydrogen peroxide / Cytoprotection by HMOX1 / response to calcium ion / protein import into nucleus / protein transport / response to estradiol / regulation of cell population proliferation / response to xenobiotic stimulus / cell cycle / inflammatory response / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Hwang, J. / Kim, M.H. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: The structural basis for the negative regulation of thioredoxin by thioredoxin-interacting protein. Authors: Hwang, J. / Suh, H.W. / Jeon, Y.H. / Hwang, E. / Nguyen, L.T. / Yeom, J. / Lee, S.G. / Lee, C. / Kim, K.J. / Kang, B.S. / Jeong, J.O. / Oh, T.K. / Choi, I. / Lee, J.O. / Kim, M.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4gfx.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4gfx.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 4gfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/4gfx ftp://data.pdbj.org/pub/pdb/validation_reports/gf/4gfx | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17057.500 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 4-154) / Mutation: F4V,K5A,K6A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TXNIP, VDUP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3M7 |
---|---|
#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.47 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.75 M sodium/potassium phosphate, 0.1 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 173 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2007 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 18976 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 90.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PARTIALLY REFINED STRUCTURE OF MSE-LABELED TXNIP N-TERMINAL DOMAIN Resolution: 1.6→18.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.815 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.152 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→18.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.644 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 16.603 Å / Origin y: -1.654 Å / Origin z: 1.97 Å
|