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- PDB-4nhk: Crystal structure of Tpa1p from Saccharomyces cerevisiae, termina... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nhk | ||||||
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Title | Crystal structure of Tpa1p from Saccharomyces cerevisiae, termination and polyadenylation protein 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA) | ||||||
![]() | PKHD-type hydroxylase TPA1 | ||||||
![]() | Oxidoreductase/Oxidoreductase inhibitor / 2-oxoglutarate oxygenase / oxygen sensing / protein synthesis regulation / double-stranded beta helix / jellyroll fold / prolyl hydroxylase / translation / ribosome / Oxidoreductase-Oxidoreductase inhibitor complex | ||||||
Function / homology | ![]() peptidyl-proline di-hydroxylation / peptidyl-proline dioxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / regulation of translational termination / poly(A) binding / L-ascorbic acid binding / Protein hydroxylation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of translational fidelity / translational termination ...peptidyl-proline di-hydroxylation / peptidyl-proline dioxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / regulation of translational termination / poly(A) binding / L-ascorbic acid binding / Protein hydroxylation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of translational fidelity / translational termination / ferrous iron binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Scotti, J.S. / McDonough, M.A. / Schofield, C.J. | ||||||
![]() | ![]() Title: Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases. Authors: Horita, S. / Scotti, J.S. / Thinnes, C. / Mottaghi-Taromsari, Y.S. / Thalhammer, A. / Ge, W. / Aik, W. / Loenarz, C. / Schofield, C.J. / McDonough, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244 KB | Display | ![]() |
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PDB format | ![]() | 193.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.7 KB | Display | ![]() |
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Full document | ![]() | 451.1 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nhlC ![]() 4nhmC ![]() 4nhxC ![]() 4nhyC ![]() 3kt7S ![]() 4nhn C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 74494.523 Da / Num. of mol.: 1 / Fragment: unp residues 21-644 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288c / Gene: TPA1, YER049W / Plasmid: pNIC28 / Production host: ![]() ![]() References: UniProt: P40032, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor | ||
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#2: Chemical | ChemComp-MN / | ||
#3: Chemical | ChemComp-PD2 / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.8 MnCl2, 1.1 mM 2,4-PDCA, 0.1 M SPG buffer, 25% PEG 1500, vapor diffusion sitting drop, temperature 293K, pH 8.0, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8344 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. all: 60504 / Num. obs: 59886 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 35.336 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.092 / Net I/σ(I): 8.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3KT7 Resolution: 1.9→48.63 Å / Occupancy max: 1 / Occupancy min: 0.5
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Displacement parameters | Biso max: 122.16 Å2 / Biso mean: 44.7557 Å2 / Biso min: 23.98 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å
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