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- PDB-5zqe: Crystal Structure of Penicillin-Binding Protein D2 from Listeria ... -
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Open data
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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 | ||||||
![]() | Lmo2812 protein | ||||||
![]() | ANTIBIOTIC / penicillin-binding protein D2 / Listeria monocytogenes / antibiotics / beta-lactams / DD-carboxypeptidase / lmo2812 / LmPBPD2 | ||||||
Function / homology | ![]() serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeong, J.H. / Kim, Y.G. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 401.6 KB | Display | ![]() |
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PDB format | ![]() | 323.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 82.4 KB | Display | |
Data in CIF | ![]() | 110.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zqaSC ![]() 5zqbC ![]() 5zqcC ![]() 5zqdC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 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.) ![]() Strain: EGD-e / Gene: lmo2812 / Production host: ![]() ![]() #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: ![]() |
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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: ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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