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Yorodumi- PDB-8jgp: Crystal structure of Deinococcus radiodurans exopolyphosphatase c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jgp | ||||||
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Title | Crystal structure of Deinococcus radiodurans exopolyphosphatase complexed with pyrophosphate | ||||||
Components | Exopolyphosphatase | ||||||
Keywords | HYDROLASE / Polyphosphate / exopolyphosphatase / pyrophosphate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 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 | 8jgp.cif.gz | 198.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jgp.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 8jgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/8jgp ftp://data.pdbj.org/pub/pdb/validation_reports/jg/8jgp | HTTPS FTP |
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-Related structure data
Related structure data | 8jgoC 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-PPV / | ||||
#3: Chemical | ChemComp-MN / | ||||
#4: Chemical | #5: Chemical | ChemComp-PO4 / | 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: 2.86 Å3/Da / Density % sol: 57.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: NaAc, NH4SO4, polyp, Mn2+ |
-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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 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: 3.02→30 Å / Num. obs: 12294 / % possible obs: 93.6 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.106 / Net I/σ(I): 8.75 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→29.14 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.02→29.14 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: 29.5833 Å / Origin y: -53.378 Å / Origin z: 0.6143 Å
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Refinement TLS group | Selection details: all |