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Yorodumi- PDB-4nhm: Crystal structure of Tpa1p from Saccharomyces cerevisiae, termina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nhm | ||||||
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Title | Crystal structure of Tpa1p from Saccharomyces cerevisiae, termination and polyadenylation protein 1, in complex with N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) | ||||||
Components | PKHD-type hydroxylase TPA1 | ||||||
Keywords | 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 | Function and homology information 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 / Protein hydroxylation / L-ascorbic acid binding / 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 / Protein hydroxylation / L-ascorbic acid binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of translational fidelity / translational termination / ferrous iron binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Scotti, J.S. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: Structure / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nhm.cif.gz | 248.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nhm.ent.gz | 197 KB | Display | PDB format |
PDBx/mmJSON format | 4nhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nhm_validation.pdf.gz | 725.4 KB | Display | wwPDB validaton report |
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Full document | 4nhm_full_validation.pdf.gz | 728.2 KB | Display | |
Data in XML | 4nhm_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 4nhm_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/4nhm ftp://data.pdbj.org/pub/pdb/validation_reports/nh/4nhm | HTTPS FTP |
-Related structure data
Related structure data | 4nhkC 4nhlC 4nhxC 4nhyC 3kt7S C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 74494.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: TPA1, YER049W / Plasmid: pNIC28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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-UN9 / | ||
#3: Chemical | ChemComp-MN / | ||
#4: Chemical | #5: 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: 2.65 Å3/Da / Density % sol: 53.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.8 mM MnCl2, 1.1 mM UN9, 0.2 M sodium citrate, 20% PEG 3350, vapor diffusion sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.2716 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / 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: 1.2716 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. all: 61684 / Num. obs: 61321 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.597 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.03 / Net I/σ(I): 9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3KT7 Resolution: 1.9→46.94 Å / Occupancy max: 1 / Occupancy min: 0.5
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Displacement parameters | Biso max: 116.52 Å2 / Biso mean: 42.4381 Å2 / Biso min: 21.92 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.94 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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