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- PDB-6f0w: prolyl hydroxylase in complex with hypoxia inducible factor oxyge... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f0w | |||||||||
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Title | prolyl hydroxylase in complex with hypoxia inducible factor oxygen degradation domain peptide fragment from Trichoplax adhaerens | |||||||||
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![]() | OXIDOREDUCTASE / Prolyl hydroxylase / oxygenase / oxygen sensing / hypoxia inducible factor | |||||||||
Function / homology | ![]() L-ascorbic acid binding / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / dioxygenase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / iron ion binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | McDonough, M.A. / Boleininger, A. / Schofield, C.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Born to sense: biophysical analyses of the oxygen sensing prolyl hydroxylase from the simplest animal Trichoplax adhaerens. Authors: Lippl, K. / Boleininger, A. / McDonough, M.A. / Abboud, M.I. / Tarhonskaya, H. / Chowdhury, R. / Loenarz, C. / Schofield, C.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.6 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.2 KB | Display | ![]() |
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Full document | ![]() | 454.9 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ey1C ![]() 3hqrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29228.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: I6QVT6 |
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#2: Protein/peptide | Mass: 2466.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-OGA / |
#4: Chemical | ChemComp-MN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 0.325 % / Description: rectangular rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20 mg/ml protein, 1mM MN(II)CL2, 2mM N-oxalylglycine, 10mM taHIF-ODD peptide, 0.31M ammonium acetate, 24% (w/v) PEG3350, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2010 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→50 Å / Num. obs: 55428 / % possible obs: 95.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.89 Å2 / Rmerge(I) obs: 0.112 / Χ2: 1.006 / Net I/σ(I): 8.5 / Num. measured all: 377792 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HQR Resolution: 1.301→37.478 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 17.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.77 Å2 / Biso mean: 20.6766 Å2 / Biso min: 8.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.301→37.478 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: 20
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