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- PDB-6z6r: 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: 6z6r | ||||||
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Title | Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, N-oxalyl-alpha-methylalanine, and factor X substrate peptide fragment(39mer-4Ser) | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakashima, Y. / Brewitz, L. / Schofield, C.J. | ||||||
![]() | ![]() Title: Synthesis of 2-oxoglutarate derivatives and their evaluation as cosubstrates and inhibitors of human aspartate/asparagine-beta-hydroxylase. Authors: Brewitz, L. / Nakashima, Y. / 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 | ![]() | 197.8 KB | Display | ![]() |
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PDB format | ![]() | 144.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yyuC ![]() 6yyvC ![]() 6yywC ![]() 6yyyC ![]() 6z6qC ![]() 5jtcS 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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1 |
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 113 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/UQK.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/UQK.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MN / |
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#4: Chemical | ChemComp-BR / ![]() |
#5: Chemical | ChemComp-GOL / ![]() |
#6: Chemical | ChemComp-UQK / |
#7: Water | ChemComp-HOH / ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.97 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Bis Tris propane, 200 mM sodium bromide, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM N-oxalyl-alpha-methylalanine, 18 mg/ml protein |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.13→50.7 Å / Num. obs: 21010 / % possible obs: 67.2 % / Redundancy: 13.2 % / Biso Wilson estimate: 35.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.175 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.13→2.29 Å / Redundancy: 12.9 % / Rmerge(I) obs: 2.09 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1051 / CC1/2: 0.493 / % possible all: 19.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5JTC Resolution: 2.13→50.7 Å / SU ML: 0.2481 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.192 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: 45.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→50.7 Å
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Refine LS restraints |
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LS refinement shell |
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