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Yorodumi- PDB-6h9j: Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPV3 (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h9j | ||||||
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Title | Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPV3 (229-255) | ||||||
Components |
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Keywords | GENE REGULATION / NON-HEME / DIOXYGENASE / OXYGENASE / METAL-BINDING / TRANSCRIPTION / DSBH / FACIAL TRIAD / ASPARAGINYL/ASPARTYL HYDROXYLASE / SIGNALING / ARD / BETA-HYDROXYLATION / ACTIVATOR-INHIBITOR / OXIDOREDUCTASE-PEPTIDE COMPLEX / OXIDOREDUCTASE ANKYRIN / CHANNEL / PROTEIN BINDING / ION CHANNEL / TRPV CHANNEL / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / negative regulation of hair cycle / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / negative regulation of hair cycle / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / osmosensory signaling pathway / oxygen sensor activity / Notch binding / TRP channels / response to temperature stimulus / negative regulation of Notch signaling pathway / positive regulation of calcium ion import / calcium ion import across plasma membrane / NF-kappaB binding / positive regulation of myoblast differentiation / actin filament organization / calcium ion transmembrane transport / ferrous iron binding / calcium channel activity / cilium / transcription corepressor activity / receptor complex / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å | ||||||
Authors | Leissing, T.M. / Clifton, I.J. / Saward, B.G. / Lu, X. / Hopkinson, R.J. / Schofield, C.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPV3 (229-255) Authors: Leissing, T.M. / Clifton, I.J. / Saward, B.G. / Lu, X. / Hopkinson, R.J. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h9j.cif.gz | 169 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h9j.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 6h9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/6h9j ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h9j | HTTPS FTP |
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-Related structure data
Related structure data | 1h2kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AD
#1: Protein | Mass: 39354.199 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 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 |
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#2: Protein/peptide | Mass: 2158.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NET8 |
-Non-polymers , 5 types, 168 molecules
#3: Chemical | ChemComp-OGA / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-ZN / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Hepes pH = 7.5, 1.8 M ammonium sulfate, 4.5% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→38.635 Å / Num. obs: 50768 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 41.46 Å2 / CC1/2: 0.9984 / Rmerge(I) obs: 0.1054 / Rpim(I) all: 0.025 / Rrim(I) all: 0.108 / Net I/σ(I): 13.74 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 20.1 % / Rmerge(I) obs: 2.854 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2483 / CC1/2: 0.497 / Rpim(I) all: 0.649 / Rrim(I) all: 2.928 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H2K Resolution: 1.83→38.635 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.4 Å2 / Biso mean: 55.7524 Å2 / Biso min: 31.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→38.635 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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