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- PDB-4zpu: The structure of DLP12 endolysin exhibits likely active and inact... -
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Basic information
Entry | Database: PDB / ID: 4zpu | ||||||
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Title | The structure of DLP12 endolysin exhibits likely active and inactive conformations. | ||||||
![]() | Lysozyme RrrD | ||||||
![]() | HYDROLASE / Endolysin / DLP12 prophage | ||||||
Function / homology | ![]() cytolysis / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to bacterium Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kesavan, B. / Arockiasamy, A. / Krishnaswamy, S. | ||||||
![]() | ![]() Title: The structure of DLP12 endolysin exhibits likely an active and inactive conformations. Authors: Kesavan, B. / Arockiasamy, A. / Krishnaswamy, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.4 KB | Display | ![]() |
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PDB format | ![]() | 108 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.4 KB | Display | ![]() |
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Full document | ![]() | 485.7 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hdeS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19052.893 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The structure of endolysin from DLP12 prophage which resides in genome of E.coli K12 Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: rrrD, arrD, ybcS, b0555, JW0544 / Production host: ![]() ![]() #2: Chemical | ChemComp-ACT / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.74 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1M Sodium acetate pH 4.8, 2.1M Sodium formate, Protein concentration-25mg/ml. |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 20% Glycerol as cryoprotectant |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 28659 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.111 / Net I/av σ(I): 23.5 / Net I/σ(I): 2.2 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HDE Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.547 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.472 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.743 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→50 Å
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Refine LS restraints |
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