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Open data
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Basic information
Entry | Database: PDB / ID: 8wt3 | ||||||
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Title | Crystal structure of peptidoglycan DL-endopeptidase CwlO | ||||||
![]() | Peptidoglycan DL-endopeptidase CwlO | ||||||
![]() | HYDROLASE / Peptidoglycan DL-endopeptidase / Autolysin | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell wall organization / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tandukar, S. / Kwon, E. / Kim, D.Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural analysis of the peptidoglycan DL-endopeptidase CwlO complexed with its inhibitory protein IseA. Authors: Tandukar, S. / Kwon, E. / Kim, D.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.8 KB | Display | ![]() |
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PDB format | ![]() | 89.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8wt4C C: citing same article ( |
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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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Components
#1: Protein | Mass: 14176.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cwlO, yvcE, yzkA, BSU34800 / Production host: ![]() ![]() References: UniProt: P40767, Hydrolases; Acting on peptide bonds (peptidases) #2: Chemical | #3: 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: 2.08 Å3/Da / Density % sol: 40.75 % |
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Crystal grow | Temperature: 293.15 K / Method: microbatch / pH: 8.5 / Details: 0.1 M Tris HCl pH 8.5 and 2.0 M ammonium sulfate |
-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 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→45.84 Å / Num. obs: 82799 / % possible obs: 93.9 % / Redundancy: 5.91 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.13→1.15 Å / Redundancy: 5.71 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 4029 / Rpim(I) all: 0.162 / Rrim(I) all: 0.396 / % possible all: 92.8 |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→45.84 Å
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Refine LS restraints |
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LS refinement shell |
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