+Open data
-Basic information
Entry | Database: PDB / ID: 8jgo | ||||||
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Title | Crystal structure of Deinococcus radiodurans exopolyphosphatase | ||||||
Components | Exopolyphosphatase | ||||||
Keywords | HYDROLASE / Polyphosphate / exopolyphosphatase | ||||||
Function / homology | Function and homology information guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity / pyrophosphatase activity / nucleobase-containing small molecule interconversion / regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zhao, Y. / Dai, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Adv Sci / Year: 2024 Title: Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling. Authors: Dai, S. / Wang, B. / Ye, R. / Zhang, D. / Xie, Z. / Yu, N. / Cai, C. / Huang, C. / Zhao, J. / Zhang, F. / Hua, Y. / Zhao, Y. / Zhou, R. / Tian, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jgo.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jgo.ent.gz | 159 KB | Display | PDB format |
PDBx/mmJSON format | 8jgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jgo_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8jgo_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8jgo_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 8jgo_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/8jgo ftp://data.pdbj.org/pub/pdb/validation_reports/jg/8jgo | HTTPS FTP |
-Related structure data
Related structure data | 8jgpC 8jgqC 8jgrC 8jgtC 8jguC 8jgwC 8jgxC 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
#1: Protein | Mass: 56831.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant) Gene: DR_A0185 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RYW9 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / | #4: 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: 2.79 Å3/Da / Density % sol: 55.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: NaAc, NH4SO4 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. obs: 49224 / % possible obs: 98 % / Redundancy: 5.34 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.067 / Net I/σ(I): 16.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.12 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.12 Å
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Refine LS restraints |
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LS refinement shell |
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