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- PDB-3ct5: Crystal and cryoEM structural studies of a cell wall degrading en... -
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Basic information
Entry | Database: PDB / ID: 3ct5 | |||||||||
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Title | Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail | |||||||||
![]() | Morphogenesis protein 1 | |||||||||
![]() | HYDROLASE / Cell wall / phi29 / infection / Late protein | |||||||||
Function / homology | ![]() virus tail, tip / virus tail fiber assembly / symbiont entry into host cell via disruption of host cell wall peptidoglycan / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / Hydrolases; Acting on peptide bonds (peptidases) / cell wall organization / metallopeptidase activity ...virus tail, tip / virus tail fiber assembly / symbiont entry into host cell via disruption of host cell wall peptidoglycan / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / Hydrolases; Acting on peptide bonds (peptidases) / cell wall organization / metallopeptidase activity / killing of cells of another organism / defense response to bacterium / proteolysis / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xiang, Y. / Rossmann, M.G. | |||||||||
![]() | ![]() Title: Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail. Authors: Ye Xiang / Marc C Morais / Daniel N Cohen / Valorie D Bowman / Dwight L Anderson / Michael G Rossmann / ![]() Abstract: The small bacteriophage phi29 must penetrate the approximately 250-A thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome ...The small bacteriophage phi29 must penetrate the approximately 250-A thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome through its tail into the bacterial cytoplasm. The tail of bacteriophage phi29 is noncontractile and approximately 380 A long. A 1.8-A resolution crystal structure of gene product 13 (gp13) shows that this tail protein has spatially well separated N- and C-terminal domains, whose structures resemble lysozyme-like enzymes and metallo-endopeptidases, respectively. CryoEM reconstructions of the WT bacteriophage and mutant bacteriophages missing some or most of gp13 shows that this enzyme is located at the distal end of the phi29 tail knob. This finding suggests that gp13 functions as a tail-associated, peptidoglycan-degrading enzyme able to cleave both the polysaccharide backbone and peptide cross-links of the peptidoglycan cell wall. Comparisons of the gp13(-) mutants with the phi29 mature and emptied phage structures suggest the sequence of events that occur during the penetration of the tail through the peptidoglycan layer. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.2 KB | Display | ![]() |
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PDB format | ![]() | 35.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 841.8 KB | Display | ![]() |
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Full document | ![]() | 842.3 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 13.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1506C ![]() 5010C ![]() 3csqC ![]() 3csrC ![]() 3cszC ![]() 3ct0C ![]() 3ct1C 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 18440.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose |
#3: Water | ChemComp-HOH / |
Sequence details | AUTORS STATE THAT RESIDUE 89 SHOULD BE ASN ACCORDING TO THEIR SEQUENCING |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG4000, 100mM Tris-HCl, 10% glycerol, 10mM NAG6, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→49.5 Å / Num. obs: 32430 / % possible obs: 98.9 % / Rmerge(I) obs: 0.05 / Rsym value: 5 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 1.37→1.42 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 8.3 / Rsym value: 19.6 / % possible all: 96.1 |
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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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.961 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→49.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.406 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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