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Open data
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Basic information
Entry | Database: PDB / ID: 5hu4 | ||||||
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Title | Cystal structure of listeria monocytogenes sortase A | ||||||
![]() | Cysteine protease | ||||||
![]() | HYDROLASE / protease / sortase A | ||||||
Function / homology | ![]() cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. | ||||||
![]() | ![]() Title: Inhibition of sortase A by chalcone prevents Listeria monocytogenes infection. Authors: Li, H. / Chen, Y. / Zhang, B. / Niu, X. / Song, M. / Luo, Z. / Lu, G. / Liu, B. / Zhao, X. / Wang, J. / Deng, 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 | ![]() | 41.1 KB | Display | ![]() |
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PDB format | ![]() | 26.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fn5S S: Starting model for refinement |
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Similar structure data |
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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
#1: Protein | Mass: 16113.419 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 78-222 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 22% w/v PEG 2000, 0.1 mol/L Tris-HCl (PH 8.5), 0.01 mol/L Ni2SO4 6H2O |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 6042 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.73 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.182 / Net I/av σ(I): 18.445 / Net I/σ(I): 11 / Num. measured all: 40438 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FN5 Resolution: 2.3→22.475 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.23 / 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: 66.25 Å2 / Biso mean: 27.3627 Å2 / Biso min: 16.14 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→22.475 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %
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