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Yorodumi- PDB-7yba: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yba | ||||||
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Title | Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-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 / response to ATP / positive regulation of calcium ion transport into cytosol / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / calcium ion transmembrane transport / regulation of protein stability / Stimuli-sensing channels / transmembrane transporter binding / cell population proliferation / electron transfer activity / negative regulation of cell population proliferation / calcium ion binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Nakashima, Y. / Brewitz, L. / Schofield, C.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate Authors: Nakashima, Y. / Brewitz, L. / 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 | 7yba.cif.gz | 296.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yba.ent.gz | 209.9 KB | Display | PDB format |
PDBx/mmJSON format | 7yba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yba_validation.pdf.gz | 794.6 KB | Display | wwPDB validaton report |
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Full document | 7yba_full_validation.pdf.gz | 800 KB | Display | |
Data in XML | 7yba_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 7yba_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/7yba ftp://data.pdbj.org/pub/pdb/validation_reports/yb/7yba | HTTPS FTP |
-Related structure data
Related structure data | 5jzaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q12797, peptide-aspartate beta-dioxygenase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-IO9 / ( |
#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: 2.98 Å3/Da / Density % sol: 58.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 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: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→86.225 Å / Num. obs: 30212 / % possible obs: 88.9 % / Redundancy: 13 % / Biso Wilson estimate: 35.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.119 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.862→2.142 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.582 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1512 / CC1/2: 0.609 / Rpim(I) all: 0.46 / Rrim(I) all: 1.65 / % possible all: 51.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JZA Resolution: 1.86→86.22 Å / SU ML: 0.1794 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6701 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: 57.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→86.22 Å
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Refine LS restraints |
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LS refinement shell |
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