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- PDB-6vcm: Crystal structure of E.coli RppH-DapF in complex with GTP, Mg2+ and F- -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vcm | ||||||
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Title | Crystal structure of E.coli RppH-DapF in complex with GTP, Mg2+ and F- | ||||||
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![]() | RNA BINDING PROTEIN/ISOMERASE / RNA degradation / RNA BINDING PROTEIN / RNA binding protein-isomerase complex | ||||||
Function / homology | ![]() diaminopimelate epimerase / diaminopimelate epimerase activity / 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 ...diaminopimelate epimerase / diaminopimelate epimerase activity / 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 / lysine biosynthetic process via diaminopimelate / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / enzyme activator activity / P-body / magnesium ion binding / protein homodimerization activity / cytoplasm / cytosol 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 | ![]() | 107.4 KB | Display | ![]() |
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PDB format | ![]() | 77.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 340.6 KB | Display | ![]() |
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Full document | ![]() | 341.9 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vckC ![]() 6vclC ![]() 6vcnC ![]() 6vcoC ![]() 6vcpC ![]() 6vcqC ![]() 6vcrC ![]() 6d1vS 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 30154.422 Da / Num. of mol.: 1 / Mutation: R36A, Y268A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: dapF, b3809, JW5592 / Production host: ![]() ![]() |
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#2: Protein | Mass: 18965.773 Da / Num. of mol.: 1 / Mutation: Q159A, E160A 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 |
-Non-polymers , 5 types, 80 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/F.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/F.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / | ||||||
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#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GTP / | #6: Chemical | ChemComp-F / | #7: 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: 4.06 Å3/Da / Density % sol: 69.74 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 9.2 / Details: 30% (v/v) PEG400, 0.1 M CHES, pH 9.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. obs: 33797 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 50.03 Å2 / CC1/2: 0.994 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.35→2.4 Å / Num. unique obs: 2208 / CC1/2: 0.65 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6D1V Resolution: 2.35→29.9 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2229 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: 61.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→29.9 Å
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Refine LS restraints |
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LS refinement shell |
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