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Yorodumi- PDB-2kdv: Solution structure of RNA Pyrophosphohydrolase RppH from Escheric... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kdv | ||||||
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Title | Solution structure of RNA Pyrophosphohydrolase RppH from Escherichia coli | ||||||
Components | RNA pyrophosphohydrolase | ||||||
Keywords | HYDROLASE / nudix family / Magnesium / Manganese / Zinc | ||||||
Function / homology | Function and homology information RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / mRNA 5'-diphosphatase activity / RNA destabilization / NAD-cap decapping / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / tRNA processing / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | minimized average, model 1 | ||||||
Model type details | minimized average | ||||||
Authors | Bi, Y. / Li, H. / Jin, C. | ||||||
Citation | Journal: To be Published Title: Solution structure of RNA pyrophosphohydrolase RppH from Escherichia coli Authors: Bi, Y. / Li, H. / Jin, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kdv.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2kdv.ent.gz | 965.8 KB | Display | PDB format |
PDBx/mmJSON format | 2kdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/2kdv ftp://data.pdbj.org/pub/pdb/validation_reports/kd/2kdv | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 19435.281 Da / Num. of mol.: 1 / Fragment: residues 1-164 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: k12 / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: Escherichia coli (E. coli) References: UniProt: P0A776, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 50mM sodium acetate-1, 20mM sodium chloride-2, 40mM DTT-3, 10mM arginine-4, 10mM glutamic-5, 0.8mM [U-13C; U-15N] RppH protein-6, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 90 / pH: 5 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: minimized average | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 21 / Representative conformer: 1 |