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- PDB-7ybb: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ybb | ||||||
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Title | Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate and factor X-derived peptide (39mer-4Ser) | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakashima, Y. / Brewitz, L. / Schofield, C.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate and factor X-derived peptide (39mer-4Ser) Authors: Nakashima, Y. / Brewitz, L. / 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 | ![]() | 222.7 KB | Display | ![]() |
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PDB format | ![]() | 150 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5jtcS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 49405.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q12797, ![]() |
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#2: Protein/peptide | ![]() Mass: 4190.384 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: F10 / Production host: ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-IO9 / ( |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.39 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.02 M Sodium/potassium phosphate, 20 % w/v Polyethylene glycol 3,350, 0.1 M Bis-Tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.68→71.39 Å / Num. obs: 41711 / % possible obs: 94.7 % / Redundancy: 13 % / Biso Wilson estimate: 16.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.072 / Rrim(I) all: 0.256 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.68→1.83 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.978 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2087 / CC1/2: 0.594 / Rpim(I) all: 0.559 / Rrim(I) all: 2.056 / % possible all: 69.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5JTC Resolution: 1.68→46.5 Å / SU ML: 0.1705 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7486 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 23.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→46.5 Å
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Refine LS restraints |
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LS refinement shell |
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