+Open data
-Basic information
Entry | Database: PDB / ID: 4s2y | ||||||
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Title | Structure of E. coli RppH bound to RNA and three magnesium ions | ||||||
Components |
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Keywords | hydrolase/RNA / Nudix hydrolase / RNA pyrophosphohydrolase / hydrolase-RNA complex | ||||||
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 | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Vasilyev, N. / Serganov, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay. Authors: Vasilyev, N. / Serganov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s2y.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s2y.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 4s2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/4s2y ftp://data.pdbj.org/pub/pdb/validation_reports/s2/4s2y | HTTPS FTP |
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-Related structure data
Related structure data | 4s2vC 4s2wSC 4s2xC 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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2 |
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Unit cell |
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-Components
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 18965.773 Da / Num. of mol.: 1 / Mutation: Q159A, E160A 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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#2: RNA chain | Mass: 1093.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Prepared by in vitro transcription |
-Non-polymers , 4 types, 124 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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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: 2.05 Å3/Da / Density % sol: 40.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: crystal growth: 0.4 M ammonium sulfate, 12% PEG 3350, 10% glycerol. crystal soaking and cross-linking: 0.02 M sodium acetate pH 5.0, 0.2 sodium sulfate, 15% PEG 3350, 15% glycerol. crystal ...Details: crystal growth: 0.4 M ammonium sulfate, 12% PEG 3350, 10% glycerol. crystal soaking and cross-linking: 0.02 M sodium acetate pH 5.0, 0.2 sodium sulfate, 15% PEG 3350, 15% glycerol. crystal soaking and cryoprotection: 0.05 M MOPS-Na pH 7.0, 0.025 M magnesium chloride, 15% PEG 3350, 25% pentaerythritol propoxylate 5/4 PO/OH, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 21164 / Num. obs: 21065 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 5 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.71 / Num. unique all: 3134 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4S2W Resolution: 1.6→19.451 Å / SU ML: 0.18 / σ(F): 1.37 / Phase error: 22.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.451 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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