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- PDB-7l0b: Crystal structure of hydroxyacyl glutathione hydrolase (GloB) fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l0b | ||||||||||||
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Title | Crystal structure of hydroxyacyl glutathione hydrolase (GloB) from Staphylococcus aureus, apoenzyme | ||||||||||||
![]() | Hydroxyacylglutathione hydrolase | ||||||||||||
![]() | HYDROLASE / GloB / esterase | ||||||||||||
Function / homology | ![]() hydroxyacylglutathione hydrolase / hydroxyacylglutathione hydrolase activity / Hydrolases / hydrolase activity Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Miller, J.J. / Jez, J.M. / Odom John, A.R. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-guided microbial targeting of antistaphylococcal prodrugs. Authors: Miller, J.J. / Shah, I.T. / Hatten, J. / Barekatain, Y. / Mueller, E.A. / Moustafa, A.M. / Edwards, R.L. / Dowd, C.S. / Planet, P.J. / Muller, F.L. / Jez, J.M. / Odom John, A.R. #1: ![]() Title: Structure-guided microbial targeting of antistaphylococcal prodrugs Authors: Miller, J.J. / Shah, I.T. / Hatten, J. / Barekatain, Y. / Mueller, E.A. / Moustafa, A.M. / Edwaards, R.L. / Dowd, C.S. / Planet, P.J. / Muller, F.L. / Jez, J.M. / Odom John, A.R. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 334.1 KB | Display | ![]() |
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PDB format | ![]() | 272.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.8 KB | Display | ![]() |
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Full document | ![]() | 469.4 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 48.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l0aC ![]() 2zwrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23735.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: W8UAH2, UniProt: A0A0D1GCF8*PLUS, hydroxyacylglutathione hydrolase, Hydrolases #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 2 uL hanging drops containing a 1:1 mixture of protein (8 mg/mL) and crystallization buffer (0.1 M imidazole pH 6.9, 0.2 M ammonium sulfate, 0.1 M calcium chloride, and 21% PEG 8k) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 195660 / % possible obs: 98.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.05 / Rrim(I) all: 0.119 / Χ2: 1.072 / Net I/σ(I): 4.8 / Num. measured all: 537795 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.939 / Num. unique obs: 5122 / CC1/2: 0.993 / Rpim(I) all: 0.041 / Rrim(I) all: 0.098 / Χ2: 2.994 / % possible all: 88.7 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZWR Resolution: 1.65→47.96 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.83 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.31 Å2 / Biso mean: 39.65 Å2 / Biso min: 17.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→47.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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