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- PDB-8jk5: Crystal structure of SP1746 from Streptococcus pneumoniae serotyp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jk5 | ||||||
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Title | Crystal structure of SP1746 from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) | ||||||
![]() | 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 | ![]() | 57 KB | Display | ![]() |
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PDB format | ![]() | 39.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jjaC ![]() 8jjkC ![]() 8jk8C ![]() 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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Unit cell |
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Components
#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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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.28 % |
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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: 1.7→59.8 Å / Num. obs: 25426 / % possible obs: 92.9 % / Redundancy: 18.4 % / CC1/2: 1 / Net I/σ(I): 41.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 1436 / CC1/2: 0.961 |
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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: 28.762 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→59.8 Å
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Refine LS restraints |
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