+Open data
-Basic information
Entry | Database: PDB / ID: 8hvj | ||||||
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Title | The structure of the E. coli mRNA endoonuclease YiCC | ||||||
Components | UPF0701 protein YicC | ||||||
Keywords | HYDROLASE / mRNA endoonuclease / yicC / mRNA metabolism | ||||||
Function / homology | Function and homology information : / RNA endonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.05 Å | ||||||
Authors | Xie, W. / Hunag, L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: The structure of the E. coli mRNA endoonuclease YiCC Authors: Xie, W. / Hunag, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hvj.cif.gz | 167 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hvj.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 8hvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hvj_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 8hvj_full_validation.pdf.gz | 471.8 KB | Display | |
Data in XML | 8hvj_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 8hvj_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/8hvj ftp://data.pdbj.org/pub/pdb/validation_reports/hv/8hvj | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33216.902 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: yicC, b3644, JW3619 / Production host: Escherichia coli (E. coli) / References: UniProt: P23839 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 24.5% PEG 3350, 0.15M Ammonium sulfate, 0.1M HEPES pH7.5, 5mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 4.05→102.6 Å / Num. obs: 9159 / % possible obs: 99.9 % / Redundancy: 8.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 4.05→4.27 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.63 / Num. unique obs: 1309 / CC1/2: 0.821 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.05→102.596 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.87 / SU B: 0.032 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 1.122 / ESU R Free: 1.346 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 196.331 Å2
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Refinement step | Cycle: LAST / Resolution: 4.05→102.596 Å
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LS refinement shell |
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