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Open data
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Basic information
Entry | Database: PDB / ID: 4k7j | ||||||
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Title | Peptidoglycan O-acetylesterase in action, 5 min | ||||||
![]() | GDSL-like Lipase/Acylhydrolase family protein | ||||||
![]() | HYDROLASE / alpha/Beta fold / peptidoglycan hydrolase | ||||||
Function / homology | ![]() Jelly Rolls - #1360 / SGNH hydrolase / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Williams, A.H. / Gomperts Boneca, I. | ||||||
![]() | ![]() Title: Visualization of a substrate-induced productive conformation of the catalytic triad of the Neisseria meningitidis peptidoglycan O-acetylesterase reveals mechanistic conservation in SGNH esterase family members. Authors: Williams, A.H. / Veyrier, F.J. / Bonis, M. / Michaud, Y. / Raynal, B. / Taha, M.K. / White, S.W. / Haouz, A. / Boneca, I.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.8 KB | Display | ![]() |
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PDB format | ![]() | 124.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459 KB | Display | ![]() |
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Full document | ![]() | 466.8 KB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 46 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40790.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EPE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.61 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Hepes pH 7.5 10-40% Peg 10000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.968→48.641 Å / Num. all: 49265 / % possible obs: 99.34 % / Observed criterion σ(F): 1.96 / Observed criterion σ(I): 1.96 |
Reflection shell | Resolution: 1.968→2.039 Å / % possible all: 99.34 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.968→48.641 Å
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Refine LS restraints |
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LS refinement shell |
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