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Open data
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Basic information
Entry | Database: PDB / ID: 8jk8 | ||||||
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Title | SP1746 in complex with UDP | ||||||
![]() | bis(5'-nucleosyl)-tetraphosphatase (symmetrical) | ||||||
![]() | HYDROLASE / enzyme / HD domain superfamily protein / phosphohydrolase / unknown gene product / SP1746 | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jin, Y. / Niu, L. / Ke, J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia. Authors: Jin, Y. / Ke, J. / Zheng, P. / Zhang, H. / Zhu, Z. / Niu, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.7 KB | Display | ![]() |
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PDB format | ![]() | 40.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jjaC ![]() 8jjkC ![]() 8jk5C ![]() 8jk9C ![]() 8jkaC ![]() 8jkpC ![]() 8jkrC ![]() 8yt5C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25051.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SP_1746 / Production host: ![]() ![]() References: UniProt: A0A0H2URF8, bis(5'-nucleosyl)-tetraphosphatase (symmetrical) |
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-Non-polymers , 6 types, 133 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-UDP / | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, sitting drop / Details: 25% PEG4000,0.15 M (NH4)2SO4,0.1 M MES pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50.01 Å / Num. obs: 17908 / % possible obs: 94.6 % / Redundancy: 18.8 % / CC1/2: 1 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 1319 / CC1/2: 0.987 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.101 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→50.01 Å
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Refine LS restraints |
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