+Open data
-Basic information
Entry | Database: PDB / ID: 3u1k | ||||||
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Title | Crystal structure of human PNPase | ||||||
Components | Polyribonucleotide nucleotidyltransferase 1, mitochondrial | ||||||
Keywords | TRANSFERASE / RNase PH / KH domain / exoribonuclease | ||||||
Function / homology | Function and homology information RNA import into mitochondrion / mitochondrial mRNA polyadenylation / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / mitochondrial RNA catabolic process / mitochondrial RNA 5'-end processing / Mitochondrial RNA degradation / positive regulation of miRNA catabolic process ...RNA import into mitochondrion / mitochondrial mRNA polyadenylation / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / mitochondrial RNA catabolic process / mitochondrial RNA 5'-end processing / Mitochondrial RNA degradation / positive regulation of miRNA catabolic process / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / poly(G) binding / nuclear polyadenylation-dependent mRNA catabolic process / positive regulation of mRNA catabolic process / regulation of cellular senescence / negative regulation of growth / rRNA import into mitochondrion / regulation of cellular respiration / RNA catabolic process / response to growth hormone / poly(U) RNA binding / miRNA binding / protein homotrimerization / mRNA catabolic process / cellular response to interferon-beta / response to cAMP / liver regeneration / mitochondrion organization / protein homooligomerization / mitochondrial intermembrane space / mRNA processing / cellular response to oxidative stress / 3'-5'-RNA exonuclease activity / regulation of cell cycle / ribosome / mitochondrial matrix / endoplasmic reticulum membrane / mitochondrion / RNA binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Lin, C.L. / Yuan, H.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Crystal structure of human polynucleotide phosphorylase: insights into its domain function in RNA binding and degradation Authors: Lin, C.L. / Wang, Y.-T. / Yang, W.-Z. / Hsiao, Y.-Y. / Yuan, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u1k.cif.gz | 497 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u1k.ent.gz | 405.6 KB | Display | PDB format |
PDBx/mmJSON format | 3u1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u1k_validation.pdf.gz | 493.4 KB | Display | wwPDB validaton report |
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Full document | 3u1k_full_validation.pdf.gz | 545.8 KB | Display | |
Data in XML | 3u1k_validation.xml.gz | 99.8 KB | Display | |
Data in CIF | 3u1k_validation.cif.gz | 141.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/3u1k ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u1k | HTTPS FTP |
-Related structure data
Related structure data | 3gcmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 68809.609 Da / Num. of mol.: 4 / Fragment: UNP residues 46-669 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PNPT1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL References: UniProt: Q8TCS8, polyribonucleotide nucleotidyltransferase #2: Chemical | ChemComp-CIT / #3: Water | ChemComp-HOH / | Sequence details | VAL 121 IS BASED ON THE NATURAL VALIANT. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10%(v/v) 2-Propanol, 0.1M Sodium citrate tribasic dihydrate, 26%(v/v) Polyethylene glycol 400 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→30 Å / Num. all: 162293 / Num. obs: 162293 / % possible obs: 100 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.39 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 2.13→2.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 4.7 / Num. unique all: 16272 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GCM Resolution: 2.13→28.5 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.839 / SU ML: 0.52 / σ(F): 1.97 / Phase error: 23.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.924 Å2 / ksol: 0.338 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.85 Å2 / Biso mean: 42.4901 Å2 / Biso min: 14.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→28.5 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: 30
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