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Yorodumi- PDB-5zqa: Crystal Structure of Penicillin-Binding Protein D2 from Listeria ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zqa | ||||||
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Title | Crystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the apo form | ||||||
Components | Lmo2812 protein | ||||||
Keywords | ANTIBIOTIC / Listeria monocytogenes / hypothetical / penicillin-binding protein / LmPBPD2 / lmo2812 | ||||||
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: 1.55 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 | 5zqa.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zqa.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 5zqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/5zqa ftp://data.pdbj.org/pub/pdb/validation_reports/zq/5zqa | HTTPS FTP |
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-Related structure data
Related structure data | 5zqbC 5zqcC 5zqdC 5zqeC 3it9S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30091.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria) Strain: EGD-e / Gene: lmo2812 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y3M3 | ||||
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#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 31.05 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M Potassium chloride, 20%(w/v) Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 17, 2014 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→37.291 Å / Num. obs: 30734 / % possible obs: 97.83 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 12.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08823 / Rrim(I) all: 0.09664 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.55→1.605 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3248 / Num. unique obs: 2508 / CC1/2: 0.861 / % possible all: 81.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3it9 Resolution: 1.55→37.291 Å / SU ML: 0.12 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 16.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→37.291 Å
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Refine LS restraints |
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LS refinement shell |
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