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Yorodumi- PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yyv | ||||||
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Title | Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese and 3-methyl-2-oxoglutarate | ||||||
Components | Aspartyl/asparaginyl beta-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / Aspartyl/asparaginyl beta-hydroxylase / Dioxygenase | ||||||
Function / homology | Function and homology information peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum ...peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum / pattern specification process / positive regulation of intracellular protein transport / activation of cysteine-type endopeptidase activity / face morphogenesis / structural constituent of muscle / positive regulation of calcium ion transport into cytosol / response to ATP / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / calcium ion homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / muscle contraction / calcium ion transmembrane transport / regulation of protein stability / Stimuli-sensing channels / cell population proliferation / transmembrane transporter binding / electron transfer activity / negative regulation of cell population proliferation / calcium ion binding / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Nakashima, Y. / Brewitz, L. / Schofield, C.J. | ||||||
Citation | Journal: Chem Sci / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yyv.cif.gz | 324.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yyv.ent.gz | 219.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/6yyv ftp://data.pdbj.org/pub/pdb/validation_reports/yy/6yyv | HTTPS FTP |
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-Related structure data
Related structure data | 6yyuC 6yywC 6yyyC 6z6qC 6z6rC 5jzaS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 49405.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASPH, BAH / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q12797, peptide-aspartate beta-dioxygenase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-Q1Z / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 200 mM magnesium acetate tetrahydrate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 3-methyl-2-oxoglutarate, 18 mg/ml protein |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→87.24 Å / Num. obs: 43399 / % possible obs: 94.2 % / Redundancy: 13.3 % / Biso Wilson estimate: 32.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.77→1.96 Å / Rmerge(I) obs: 1.876 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2170 / CC1/2: 0.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JZA Resolution: 1.77→43.62 Å / SU ML: 0.1687 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5691
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→43.62 Å
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Refine LS restraints |
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LS refinement shell |
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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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