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Open data
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Basic information
Entry | Database: PDB / ID: 8wmy | ||||||
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Title | Crystal structure of YqeK in complex with MG and ADP. | ||||||
![]() | bis(5'-nucleosyl)-tetraphosphatase (symmetrical) | ||||||
![]() | HYDROLASE / Staphylococcus pyogenes / YqeK / Protein structure / enzymatic activity. | ||||||
Function / homology | bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / Ap4A hydrolase / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / hydrolase activity / ADENOSINE-5'-DIPHOSPHATE / bis(5'-nucleosyl)-tetraphosphatase (symmetrical)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mo, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular Mechanism of Ap4A Hydrolysis by YqeK of Staphylococcus pyogenes. Authors: Mo, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.3 KB | Display | ![]() |
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PDB format | ![]() | 75.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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Components
#1: Protein | Mass: 22487.834 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sequence reference for Staphylococcus aureus is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A4U7IGH6. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A4U7IGH6, bis(5'-nucleosyl)-tetraphosphatase (symmetrical) #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 293.15 K / Method: evaporation Details: 12% 2-propannol, 18.5% PEG-4000 and 100 mM sodium HEPES (pH 7.4) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→35.04 Å / Num. obs: 35345 / % possible obs: 98.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.17 Å2 / CC1/2: 0.98 / Net I/σ(I): 3 |
Reflection shell | Resolution: 1.91→1.978 Å / Num. unique obs: 3499 / CC1/2: 0.97 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→35.04 Å
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Refine LS restraints |
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LS refinement shell |
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