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Yorodumi- PDB-6qa5: Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in the apo form -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qa5 | ||||||
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Title | Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in the apo form | ||||||
Components | Aspartyl/asparaginyl beta-hydroxylase | ||||||
Keywords | GENE REGULATION / OXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / 2-OXOGLUTARATE DEPENDENT OXYGENASE / OXYGENASE / HYPOXIA / METAL-BINDING / TRANSCRIPTION / ASPARTYL/ASPARAGINYL BETA-2 HYDROXYLASE / ASPH / EGF-LIKE DOMAIN HYDROXYLASE / DOUBLE STRANDED BETA-HELIX / FACIAL TRIAD / CYTOPLASM / TPR / TETRATRICOPEPTIDE REPEAT / BETA-HYDROXYLATION / SIGNALING / DEVELOPMENT / VITAMIN C | ||||||
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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / limb morphogenesis ...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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / limb morphogenesis / 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: 2.655 Å | ||||||
Authors | Chowdhury, R. / Pfeffer, I. / Schofield, C.J. | ||||||
Citation | Journal: To Be Published Title: Apo aspH-H679A Authors: Pfeffer, I. / Chowdhury, R. / 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 | 6qa5.cif.gz | 256.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qa5.ent.gz | 209.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/6qa5 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/6qa5 | HTTPS FTP |
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-Related structure data
Related structure data | 6q9fS S: Starting model for refinement |
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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: 49338.270 Da / Num. of mol.: 1 / Mutation: H679A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASPH, BAH / Plasmid: PET-28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q12797, peptide-aspartate beta-dioxygenase | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M PCTP (Propionic acid, Cacodylate, Bis-tris propane) buffer pH 9.0 25 % w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→44.718 Å / Num. obs: 18051 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 40.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.084 / Rrim(I) all: 0.251 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.319 / Mean I/σ(I) obs: 2 / Num. unique obs: 1770 / CC1/2: 0.608 / Rpim(I) all: 0.478 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q9F Resolution: 2.655→44.718 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 56.3 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.655→44.718 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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