[English] 日本語
Yorodumi- PDB-8jgr: Crystal structure of Deinococcus radiodurans exopolyphosphatase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jgr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Deinococcus radiodurans exopolyphosphatase in the presence of Pi | ||||||
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: 2.5 Å | ||||||
Authors | Zhao, Y. / Dai, S. | ||||||
Funding support | China, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jgr.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jgr.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 8jgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jgr_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jgr_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8jgr_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 8jgr_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/8jgr ftp://data.pdbj.org/pub/pdb/validation_reports/jg/8jgr | HTTPS FTP |
-Related structure data
Related structure data | 8jgoC 8jgpC 8jgqC 8jgtC 8jguC 8jgwC 8jgxC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.59 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: NaH2PO4, K2HPO4 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→30 Å / Num. obs: 20449 / % possible obs: 94.4 % / Redundancy: 5.94 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.067 / Net I/σ(I): 17.76 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.58 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.33 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|