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Yorodumi- PDB-5ygu: Crystal structure of Escherichia coli (strain K12) mRNA Decapping... -
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-Basic information
Entry | Database: PDB / ID: 5ygu | ||||||
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Title | Crystal structure of Escherichia coli (strain K12) mRNA Decapping Complex RppH-DapF | ||||||
Components |
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Keywords | ISOMERASE/HYDROLASE / RppH-DapF / Decapping / Hydrolase / ISOMERASE-HYDROLASE complex | ||||||
Function / homology | Function and homology information diaminopimelate epimerase / diaminopimelate epimerase activity / RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / mRNA 5'-diphosphatase activity / NAD-cap decapping / 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 / mRNA 5'-diphosphatase activity / NAD-cap decapping / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å | ||||||
Authors | Wang, Q. / Guan, Z.Y. / Zhang, D.L. / Zou, T.T. / Yin, P. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli. Authors: Wang, Q. / Zhang, D. / Guan, Z. / Li, D. / Pei, K. / Liu, J. / Zou, T. / Yin, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ygu.cif.gz | 187.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ygu.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ygu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/5ygu ftp://data.pdbj.org/pub/pdb/validation_reports/yg/5ygu | HTTPS FTP |
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-Related 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: 30245.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: dapF, b3809, JW5592 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6K1, diaminopimelate epimerase | ||
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#2: Protein | Mass: 20067.920 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-158 / Mutation: C16S 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A776, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||
#3: Chemical | ChemComp-TLA / | ||
#4: Chemical | ChemComp-IOD / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.7 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Potassium Sodium Tartrate, Sodium Iodine, Xylitol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. obs: 30026 / % possible obs: 99.8 % / Redundancy: 14 % / Net I/σ(I): 18.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4S2V, 4IJZ Resolution: 2.298→47.985 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.298→47.985 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.2964 Å / Origin y: 5.6066 Å / Origin z: 21.3458 Å
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Refinement TLS group | Selection details: all |