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Open data
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Basic information
Entry | Database: PDB / ID: 5nm7 | |||||||||
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Title | Crystal structure of Burkholderia AP3 phage endolysin | |||||||||
![]() | Peptidoglycan-binding domain 1 | |||||||||
![]() | HYDROLASE / peptidoglycan binding domain / lysozyme family | |||||||||
Function / homology | ![]() N-acetylmuramidase / N-acetylmuramidase / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zrubek, K. / Wisniewska, M. / Rembacz, K. / Maciejewska, B. / Drulis-Kawa, Z. / Dubin, G. | |||||||||
![]() | ![]() Title: Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue. Authors: Maciejewska, B. / Zrubek, K. / Espaillat, A. / Wisniewska, M. / Rembacz, K.P. / Cava, F. / Dubin, G. / Drulis-Kawa, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.7 KB | Display | ![]() |
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PDB format | ![]() | 89.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.7 KB | Display | ![]() |
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Full document | ![]() | 463.4 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 3 - 263 / Label seq-ID: 3 - 263
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Components
#1: Protein | Mass: 28987.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GLY / #3: Chemical | ChemComp-PGE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG pH 7.0, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→26.72 Å / Num. obs: 61070 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 3.3 / CC1/2: 0.791 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.162 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→26.72 Å
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Refine LS restraints |
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