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Open data
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Basic information
Entry | Database: PDB / ID: 6vcn | ||||||
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Title | Crystal structure of E.coli RppH in complex with ppcpG | ||||||
![]() | RNA pyrophosphohydrolase | ||||||
![]() | RNA BINDING PROTEIN / RNA degradation | ||||||
Function / homology | ![]() RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / NAD-cap decapping / mRNA 5'-diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / tRNA processing / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / NAD-cap decapping / mRNA 5'-diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / tRNA processing / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / P-body / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH. Authors: Gao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.7 KB | Display | ![]() |
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PDB format | ![]() | 35.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 353.9 KB | Display | ![]() |
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Full document | ![]() | 353.6 KB | Display | |
Data in XML | ![]() | 1.7 KB | Display | |
Data in CIF | ![]() | 4.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vckC ![]() 6vclC ![]() 6vcmC ![]() 6vcoC ![]() 6vcpC ![]() 6vcqC ![]() 6vcrC ![]() 4s2yS C: citing same article ( 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 on special symmetry positions |
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Components
#1: Protein | Mass: 18964.723 Da / Num. of mol.: 1 / Mutation: K149A, E150A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: ![]() ![]() References: UniProt: P0A776, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||||
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#2: Chemical | ChemComp-G2P / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.5 M NH4Cl, 10% (v/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.48 Å / Num. obs: 12944 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 20.98 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Num. unique obs: 1244 / CC1/2: 0.718 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4S2Y Resolution: 1.9→19.48 Å / SU ML: 0.2545 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.7136 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: 26.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.48 Å
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Refine LS restraints |
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LS refinement shell |
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