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- PDB-8hvq: Crystal structure of haloacid dehalogenase-like hydrolase family ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hvq | ||||||
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Title | Crystal structure of haloacid dehalogenase-like hydrolase family enzyme from Staphylococcus lugdunensis | ||||||
![]() | Cof-type HAD-IIB family hydrolase | ||||||
![]() | HYDROLASE / phosphatase / acidic pH / HAD family enzyme / Staphylococcus | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kaur, H. / Mahto, J.K. / Kumar, P. / Sharma, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of haloacid dehalogenase superfamily acid phosphatase from Staphylococcus lugdunensis. Authors: Kaur, H. / Rode, S. / Kp, S. / Mahto, J.K. / Alam, M.S. / Gupta, D.N. / Kar, B. / Singla, J. / Kumar, P. / Sharma, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.2 KB | Display | ![]() |
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PDB format | ![]() | 180.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.5 KB | Display | ![]() |
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Full document | ![]() | 500 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 40.4 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26244.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 626 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OXM.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OXM.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M sodium formate, 0.2M ammonium acetate, 0.2M sodium citrate tribasic dihydrate, 0.2M sodium potassium tartrate tetrahydrate, 0.2M sodium oxamate, 10% w/v PEG 4000, 20% v/v glycerol, 0.1M MES/imidazole pH 6.5 |
-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: Apr 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→58.86 Å / Num. obs: 62991 / % possible obs: 98.6 % / Redundancy: 1.8 % / CC1/2: 0.997 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.73→1.76 Å / Num. unique obs: 3498 / CC1/2: 0.895 |
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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: 22.82 Å2
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Refinement step | Cycle: 1 / Resolution: 1.73→58.86 Å
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Refine LS restraints |
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