[English] 日本語
Yorodumi- PDB-4jaa: Factor inhibiting HIF-1 alpha in complex with consensus ankyrin r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jaa | ||||||
---|---|---|---|---|---|---|---|
Title | Factor inhibiting HIF-1 alpha in complex with consensus ankyrin repeat domain-(d)LEU peptide | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE/PEPTIDE / NON-HEME / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / ASPARAGINYL / ASPARTYL HYDROXYLASE / EPIGENETIC REGULATION / SIGNALING / ARD / BETA-HYDROXYLATION / ACTIVATOR/INHIBITOR / OXIDOREDUCTASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity / Notch binding / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å | ||||||
Authors | Scotti, J.S. / Ge, W. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: To be Published Title: Structure of an oxygenase in complex with substrate Authors: Scotti, J.S. / Ge, W. / McDonough, M.A. / Schofield, C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jaa.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jaa.ent.gz | 124.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jaa_validation.pdf.gz | 470.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4jaa_full_validation.pdf.gz | 472.9 KB | Display | |
Data in XML | 4jaa_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 4jaa_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/4jaa ftp://data.pdbj.org/pub/pdb/validation_reports/ja/4jaa | HTTPS FTP |
-Related structure data
Related structure data | 4nr1C 1h2kS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AS
#1: Protein | Mass: 40328.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase |
---|---|
#2: Protein/peptide | Mass: 2231.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide. |
-Non-polymers , 4 types, 124 molecules
#3: Chemical | ChemComp-ZN / | ||
---|---|---|---|
#4: Chemical | ChemComp-OGA / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.56 % / Mosaicity: 0.72 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6M AMMONIUM SULPHATE, 6% PEG 400, 0.1M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2012 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→33.804 Å / Num. obs: 22451 / % possible obs: 99.3 % / Redundancy: 5 % / Biso Wilson estimate: 44.565 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.39→2.55 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3937 / % possible all: 98.7 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H2K Resolution: 2.39→33.8 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8386 / SU ML: 0.28 / σ(F): 1.33 / Phase error: 22.96 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.74 Å2 / Biso mean: 41.6862 Å2 / Biso min: 13.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.39→33.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|