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- PDB-5jza: Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR dom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jza | ||||||
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Title | Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese and N-oxalylglycine | ||||||
![]() | Aspartyl/asparaginyl beta-hydroxylase | ||||||
![]() | OXIDOREDUCTASE / 2-oxoglutarate dependent oxygenase / aspartyl/asparaginyl beta-hydroxylase / EGF-like domain hydroxylase / double stranded beta-helix / tetratricopeptide repeat | ||||||
Function / homology | ![]() 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 / transmembrane transporter binding / cell population proliferation / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McDonough, M.A. / Pfeffer, I. | ||||||
![]() | ![]() Title: Aspartate/asparagine-beta-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern. Authors: Pfeffer, I. / Brewitz, L. / Krojer, T. / Jensen, S.A. / Kochan, G.T. / Kershaw, N.J. / Hewitson, K.S. / McNeill, L.A. / Kramer, H. / Munzel, M. / Hopkinson, R.J. / Oppermann, U. / Handford, ...Authors: Pfeffer, I. / Brewitz, L. / Krojer, T. / Jensen, S.A. / Kochan, G.T. / Kershaw, N.J. / Hewitson, K.S. / McNeill, L.A. / Kramer, H. / Munzel, M. / Hopkinson, R.J. / Oppermann, U. / Handford, P.A. / McDonough, M.A. / 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 | ![]() | 195.7 KB | Display | ![]() |
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PDB format | ![]() | 153.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.5 KB | Display | ![]() |
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Full document | ![]() | 451.9 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5apaSC ![]() 5jqyC ![]() 5jz6C ![]() 5jz8C ![]() 5jzuC ![]() 6rk9C 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: 49405.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q12797, peptide-aspartate beta-dioxygenase | ||||
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#2: Chemical | ChemComp-MN / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-OGA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 100 mM bicine, 100 mM sodium chloride, 27% PEG 550 MME, 1 mM manganese chloride, 2 mM N-oxalylglycine, 18 mg/ml protein |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→85.21 Å / Num. obs: 33179 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 46.25 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5APA Resolution: 2.14→85.21 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.18 Å2 / Biso mean: 68.3722 Å2 / Biso min: 31.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.14→85.21 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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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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