+Open data
-Basic information
Entry | Database: PDB / ID: 8akh | |||||||||
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Title | Crystal structure of DltE from L. plantarum soaked with LTA | |||||||||
Components | Beta-lactamase family protein | |||||||||
Keywords | CELL CYCLE / carboxyesterase / D-alanylation / lipoteichoic acids | |||||||||
Function / homology | serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / SN-GLYCEROL-3-PHOSPHATE / L(+)-TARTARIC ACID / Serine-type D-Ala-D-Ala carboxypeptidase Function and homology information | |||||||||
Biological species | Lactiplantibacillus plantarum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Ravaud, S. / Nikolopoulos, N. / Grangeasse, C. | |||||||||
Funding support | France, 2items
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Citation | Journal: Elife / Year: 2023 Title: Structure-function analysis of Lactiplantibacillus plantarum DltE& reveals D-alanylated lipoteichoic acids as direct cues supporting Drosophila juvenile growth. Authors: Nikolopoulos, N. / Matos, R. / Ravaud, S. / Courtin, P. / Akherraz, H. / Palussiere, S. / Gueguen-Chaignon, V. / Salomon-Mallet, M. / Guillot, A. / Guerardel, Y. / Chapot-Chartier, M.P. / ...Authors: Nikolopoulos, N. / Matos, R. / Ravaud, S. / Courtin, P. / Akherraz, H. / Palussiere, S. / Gueguen-Chaignon, V. / Salomon-Mallet, M. / Guillot, A. / Guerardel, Y. / Chapot-Chartier, M.P. / Grangeasse, C. / Leulier, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8akh.cif.gz | 321.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8akh.ent.gz | 210.6 KB | Display | PDB format |
PDBx/mmJSON format | 8akh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8akh_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8akh_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8akh_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 8akh_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/8akh ftp://data.pdbj.org/pub/pdb/validation_reports/ak/8akh | HTTPS FTP |
-Related structure data
Related structure data | 8agrSC 8aikC 8ajiC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 41822.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactiplantibacillus plantarum (bacteria) Gene: pbpX2, pbpX_4, C7M36_02596, E3O64_07015, E3U93_06380, FEE41_04205, IV39_GL001648, LPJSA22_01868, SN35N_2987 Production host: Escherichia coli (E. coli) References: UniProt: A0A0P7JVD2, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-G3P / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.03 Å / Num. obs: 139817 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 15.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.022 / Net I/σ(I): 16.61 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.4422 / Num. unique obs: 13770 / CC1/2: 0.678 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8AGR Resolution: 1.4→48.03 Å / SU ML: 0.1488 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.239 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: 19.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→48.03 Å
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Refine LS restraints |
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LS refinement shell |
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