+Open data
-Basic information
Entry | Database: PDB / ID: 8agr | |||||||||
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Title | Crystal structure of DltE from L. plantarum, apo form | |||||||||
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 / Serine-type D-Ala-D-Ala carboxypeptidase Function and homology information | |||||||||
Biological species | Lactiplantibacillus plantarum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 | 8agr.cif.gz | 165.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8agr.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 8agr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8agr_validation.pdf.gz | 457.1 KB | Display | wwPDB validaton report |
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Full document | 8agr_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 8agr_validation.xml.gz | 33 KB | Display | |
Data in CIF | 8agr_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8agr ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8agr | HTTPS FTP |
-Related structure data
Related structure data | 8aikC 8ajiC 8akhC 3wwxS 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 | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.35 Å3/Da / Density % sol: 47.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG MME 5K, Tris pH8.5, LiSO4, ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→47.86 Å / Num. obs: 64951 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rpim(I) all: 0.12 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.86→1.9 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 39993 / Rpim(I) all: 0.441 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WWX Resolution: 1.86→47.796 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.165 / SU B: 2.901 / SU ML: 0.086 / Average fsc free: 0.9732 / Average fsc work: 0.9822 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.12 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.051 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→47.796 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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