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Open data
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Basic information
Entry | Database: PDB / ID: 8qzg | |||||||||
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Title | 1,3 L,D-transpeptidase from Gluconobacter oxydans | |||||||||
![]() | YkuD domain-containing protein | |||||||||
![]() | TRANSFERASE / transpeptidase / peptidoglycan / Gluconobacter oxydans / cell wall / antibiotics resistance / lipoprotein | |||||||||
Function / homology | L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / peptidoglycan L,D-transpeptidase activity / peptidoglycan biosynthetic process / transferase activity / YkuD domain-containing protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | ter Beek, J. / Berntsson, R.P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria. Authors: Espaillat, A. / Alvarez, L. / Torrens, G. / Ter Beek, J. / Miguel-Ruano, V. / Irazoki, O. / Gago, F. / Hermoso, J.A. / Berntsson, R.P. / Cava, F. #1: ![]() Title: A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha and Betaproteobacteria Authors: Espaillat, A. / Alvarez, L. / Torrens, G. / Beek, J.T. / Miguel-Ruano, V. / Irazoki, O. / Gago, F. / Hermoso, J.A. / Berntsson, R.P.A. / Cava, F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.1 KB | Display | ![]() |
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PDB format | ![]() | 130.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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
#1: Protein | Mass: 36058.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Imidazole MES monohydrate (acid) pH 6.5, 30 mM Magnesium chloride hexahydrate, 30 mM Calcium chloride dihydrate, 20% v/v PEG 500* MME; 10 % w/v PEG 20000 (Morpheus A1 condition) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→48.41 Å / Num. obs: 29339 / % possible obs: 98.48 % / Observed criterion σ(I): 1.12 / Redundancy: 5.6 % / Biso Wilson estimate: 24.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1108 / Net I/σ(I): 10.48 |
Reflection shell | Resolution: 1.732→1.794 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.12 / Num. unique obs: 2614 / CC1/2: 0.383 / CC star: 0.744 / % possible all: 88.03 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 27.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→48.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.7260309625 Å / Origin y: 0.229446970295 Å / Origin z: -1.25038284205 Å
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Refinement TLS group | Selection details: { A|54-B|1 } |