+Open data
-Basic information
Entry | Database: PDB / ID: 7w89 | ||||||
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Title | The structure of Deinococcus radiodurans Yqgf | ||||||
Components | Putative pre-16S rRNA nuclease | ||||||
Keywords | HYDROLASE / RNase / RNA binding | ||||||
Function / homology | Function and homology information rRNA 5'-end processing / nuclease activity / Hydrolases; Acting on ester bonds / cytoplasm Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.50006105724 Å | ||||||
Authors | Cheng, K. | ||||||
Funding support | China, 1items
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Citation | Journal: Mbio / Year: 2022 Title: Biochemical and Structural Study of RuvC and YqgF from Deinococcus radiodurans. Authors: Sun, Y. / Yang, J. / Xu, G. / Cheng, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w89.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w89.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 7w89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w89_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 7w89_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 7w89_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 7w89_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/7w89 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/7w89 | HTTPS FTP |
-Related structure data
Related structure data | 7w8dC 1ovqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 14841.159 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: DR_2509 / Production host: Escherichia coli (E. coli) References: UniProt: Q9RRI2, Hydrolases; Acting on ester bonds |
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#2: 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: 2 Å3/Da / Density % sol: 38.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MgCl2, 0.1M HEPES (pH 7.0), 15% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→27.07 Å / Num. obs: 19580 / % possible obs: 93.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 26.04 |
Reflection shell | Resolution: 1.5→1.54 Å / Rmerge(I) obs: 0.132 / Num. unique obs: 1430 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OVQ Resolution: 1.50006105724→27.0688711921 Å / SU ML: 0.11487136053 / Cross valid method: FREE R-VALUE / σ(F): 1.4025631195 / Phase error: 18.1688009337 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: 15.6326682596 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.50006105724→27.0688711921 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: 79.2987867651 Å / Origin y: 0.666036948163 Å / Origin z: 41.8795882323 Å
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Refinement TLS group | Selection details: all |