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Open data
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Basic information
Entry | Database: PDB / ID: 7sp3 | ||||||
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Title | E. coli RppH bound to Ap4A | ||||||
![]() | RNA pyrophosphohydrolase | ||||||
![]() | RNA BINDING PROTEIN / Cap / Ap4A / RppH / Nudix hydrolase | ||||||
Function / homology | ![]() pyrophosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Serganov, A.A. / Vasilyev, N. / Nuthanakanti, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A distinct RNA recognition mechanism governs Np 4 decapping by RppH. Authors: Levenson-Palmer, R. / Luciano, D.J. / Vasilyev, N. / Nuthanakanti, A. / Serganov, A. / Belasco, J.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.8 KB | Display | ![]() |
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PDB format | ![]() | 35 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4s2wS 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18965.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rppH, nudH, D9D94_13650, D9E88_05455, D9J61_06705, G5V60_04980, GP711_07030 Production host: ![]() ![]() References: UniProt: A0A3K0QF38, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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-Non-polymers , 5 types, 118 molecules ![](data/chem/img/B4P.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/F.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/F.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-B4P / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-F / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.4 M (NH4)2SO4, 10% (v/v) PEG3350, and 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.4 Å / Num. obs: 20993 / % possible obs: 97.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 18.88 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.021 / Rrim(I) all: 0.048 / Net I/σ(I): 22.49 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.5874 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1890 / CC1/2: 0.752 / CC star: 0.926 / Rpim(I) all: 0.3048 / Rrim(I) all: 0.6652 / % possible all: 89.32 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4S2W Resolution: 1.6→18.84 Å / SU ML: 0.197 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.9407 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→18.84 Å
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Refine LS restraints |
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LS refinement shell |
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