[English] 日本語
Yorodumi- PDB-6ruj: Factor inhibiting HIF-1 alpha in complex with consensus ankyrin r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ruj | ||||||
---|---|---|---|---|---|---|---|
Title | Factor inhibiting HIF-1 alpha in complex with consensus ankyrin repeat domain-(d)3-hydroxy-Leu peptide | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / 2-OG-dependent dioxygenase | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Nakashima, Y. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: Commun Chem / Year: 2020 Title: A human protein hydroxylase that accepts D-residues Authors: Choi, H. / Hardy, A. / Leissing, T.M. / Chowdhury, R. / Ge, W. / Markoulides, M. / Scotti, J.S. / Thorbjornsrud, H. / Nakashima, Y. / Kang, D. / Hong, S. / Lee, J. / Park, H. / McDonough, M.A. / Schofield, C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ruj.cif.gz | 223.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ruj.ent.gz | 182.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ruj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ruj_validation.pdf.gz | 998.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ruj_full_validation.pdf.gz | 1003.1 KB | Display | |
Data in XML | 6ruj_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6ruj_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/6ruj ftp://data.pdbj.org/pub/pdb/validation_reports/ru/6ruj | HTTPS FTP |
-Related structure data
Related structure data | 1h2kS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one ...References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
---|---|
#2: Protein/peptide | Mass: 1623.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 98 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: 3.25 Å3/Da / Density % sol: 62.1 % |
---|---|
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 / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97942 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→73.63 Å / Num. obs: 22013 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 60.458 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.154 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.42→2.46 Å / Redundancy: 13.4 % / Rmerge(I) obs: 2.367 / Mean I/σ(I) obs: 1 / Num. unique obs: 1051 / CC1/2: 0.557 / Rpim(I) all: 0.668 / Rrim(I) all: 2.461 / % possible all: 98.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H2K Resolution: 2.42→56.042 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.64
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→56.042 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|