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- PDB-8rhf: Lytic Transglycosylase MltD of Pseudomonas aeruginosa bound to th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rhf | ||||||
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Title | Lytic Transglycosylase MltD of Pseudomonas aeruginosa bound to the Natural Product Bulgecin A, with two LysM domains | ||||||
![]() | LysM peptidoglycan-binding domain-containing protein | ||||||
![]() | LYASE / Lytic transglycosylase / Bacterial cell-wall / bulgecin A | ||||||
Function / homology | ![]() Lyases; Carbon-oxygen lyases; Acting on polysaccharides / lytic transglycosylase activity / peptidoglycan metabolic process / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miguel-Ruano, V. / Hermoso, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of lytic transglycosylase MltD of Pseudomonas aeruginosa, a target for the natural product bulgecin A. Authors: Miguel-Ruano, V. / Feltzer, R. / Batuecas, M.T. / Ramachandran, B. / El-Araby, A.M. / Avila-Cobian, L.F. / De Benedetti, S. / Mobashery, S. / Hermoso, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 289.1 KB | Display | ![]() |
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PDB format | ![]() | 232.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rheC ![]() 8rhiC 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: 38579.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: His tag and TEV cleavage site in the N-t region. MltD contruction from residues 76 to 393 Source: (gene. exp.) ![]() ![]() Gene: mltD, CAZ10_25765, CGU42_31890, GNQ48_00460, GUL26_19730, IPC1295_05870, PAERUG_P19_London_7_VIM_2_05_10_06006 Production host: ![]() ![]() References: UniProt: A0A0C7CWY9, Lyases; Carbon-oxygen lyases; Acting on polysaccharides #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 25% w/v PEG 550 MME, and 10 mM zinc sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→60.62 Å / Num. obs: 52231 / % possible obs: 83.04 % / Redundancy: 12.47 % / CC1/2: 0.997 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 1.476 / Num. unique obs: 2611 / CC1/2: 0.5522 |
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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: 37.083 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→60.62 Å
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Refine LS restraints |
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