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Yorodumi- PDB-5zqe: Crystal Structure of Penicillin-Binding Protein D2 from Listeria ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zqe | ||||||
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Title | Crystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the Cefuroxime bound form | ||||||
Components | Lmo2812 protein | ||||||
Keywords | ANTIBIOTIC / penicillin-binding protein D2 / Listeria monocytogenes / antibiotics / beta-lactams / DD-carboxypeptidase / lmo2812 / LmPBPD2 | ||||||
Function / homology | Function and homology information serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis Similarity search - Function | ||||||
Biological species | Listeria monocytogenes EGD-e (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 Å | ||||||
Authors | Jeong, J.H. / Kim, Y.G. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Antimicrob. Agents Chemother. / Year: 2018 Title: Crystal Structures of Penicillin-Binding Protein D2 from Listeria monocytogenes and Structural Basis for Antibiotic Specificity Authors: Jeong, J.H. / Cha, H.J. / Kim, Y.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zqe.cif.gz | 401.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zqe.ent.gz | 323.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/5zqe ftp://data.pdbj.org/pub/pdb/validation_reports/zq/5zqe | HTTPS FTP |
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-Related structure data
Related structure data | 5zqaSC 5zqbC 5zqcC 5zqdC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 30091.605 Da / Num. of mol.: 8 / Fragment: UNP residues 21-272 Source method: isolated from a genetically manipulated source Details: it contains covalently bound cefuroxime molecules Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria) Strain: EGD-e / Gene: lmo2812 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y3M3 #2: Chemical | ChemComp-CES / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2016 |
Radiation | Monochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.996→29.982 Å / Num. obs: 149025 / % possible obs: 91.13 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 13.29 Å2 / Rsym value: 0.127 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.996→2.067 Å / Redundancy: 5.9 % / Num. unique obs: 14478 / Rsym value: 0.475 / % possible all: 84.24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZQA Resolution: 1.996→29.982 Å / Cross valid method: NONE / σ(F): 0 / Phase error: 38.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.996→29.982 Å
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Refine LS restraints |
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LS refinement shell |
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