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Yorodumi- PDB-8jgu: Crystal structure of N-terminal domain of exopolyphosphatase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jgu | ||||||
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Title | Crystal structure of N-terminal domain of exopolyphosphatase from Deinococcus radiodurans | ||||||
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: 1.99 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 | 8jgu.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jgu.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 8jgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jgu_validation.pdf.gz | 853.2 KB | Display | wwPDB validaton report |
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Full document | 8jgu_full_validation.pdf.gz | 855 KB | Display | |
Data in XML | 8jgu_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 8jgu_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/8jgu ftp://data.pdbj.org/pub/pdb/validation_reports/jg/8jgu | HTTPS FTP |
-Related structure data
Related structure data | 8jgoC 8jgpC 8jgqC 8jgrC 8jgtC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35814.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal domain of wild-type protein 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-NA / |
#3: 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: 2.04 Å3/Da / Density % sol: 39.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaAc |
-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: Jul 3, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.99→30 Å / Num. obs: 19639 / % possible obs: 98 % / Redundancy: 7.05 % / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.12 / Net I/σ(I): 17.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→29.27 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.92 / 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: 1.99→29.27 Å
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Refine LS restraints |
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LS refinement shell |
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