+Open data
-Basic information
Entry | Database: PDB / ID: 6vcp | ||||||
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Title | Crystal structure of E.coli RppH in complex with UTP | ||||||
Components | RNA pyrophosphohydrolase | ||||||
Keywords | RNA BINDING PROTEIN / RNA degradation | ||||||
Function / homology | Function and homology information RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / mRNA 5'-diphosphatase activity / 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 S88 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Gao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vcp.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vcp.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vcp_validation.pdf.gz | 390.3 KB | Display | wwPDB validaton report |
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Full document | 6vcp_full_validation.pdf.gz | 390.5 KB | Display | |
Data in XML | 6vcp_validation.xml.gz | 1.5 KB | Display | |
Data in CIF | 6vcp_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/6vcp ftp://data.pdbj.org/pub/pdb/validation_reports/vc/6vcp | HTTPS FTP |
-Related structure data
Related structure data | 6vckC 6vclC 6vcmC 6vcnC 6vcoC 6vcqC 6vcrC 4s2yS 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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Unit cell |
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-Components
#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 S88 (bacteria) / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A776, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.4 M (NH4)2SO4, 10% (v/v) PEG3350, 10% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 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: 1.7→19.37 Å / Num. obs: 19245 / % possible obs: 99.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Num. unique obs: 1896 / CC1/2: 0.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4S2Y Resolution: 1.7→19.37 Å / SU ML: 0.1638 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6711
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.37 Å
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Refine LS restraints |
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LS refinement shell |
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