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Yorodumi- PDB-3csq: Crystal and cryoEM structural studies of a cell wall degrading en... -
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-Basic information
Entry | Database: PDB / ID: 3csq | ||||||
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Title | Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail | ||||||
Components | Morphogenesis protein 1 | ||||||
Keywords | HYDROLASE / infection / phi29 / Late protein | ||||||
Function / homology | Function and homology information 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 | Bacteriophage phi-29 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR, SAD / Resolution: 1.8 Å | ||||||
Authors | Xiang, Y. / Rossmann, M.G. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3csq.cif.gz | 263.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3csq.ent.gz | 214.4 KB | Display | PDB format |
PDBx/mmJSON format | 3csq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/3csq ftp://data.pdbj.org/pub/pdb/validation_reports/cs/3csq | HTTPS FTP |
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-Related structure data
Related structure data | 1506C 5010C 3csrC 3cszC 3ct0C 3ct1C 3ct5C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 37648.074 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteriophage phi-29 (virus) / Gene: 13 / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Codon plus RP / References: UniProt: P15132 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Sequence details | AUTORS STATE THAT RESIDUE 89 SHOULD BE ASN ACCORDING TO THEIR SEQUENCING | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100mM Tris-HCl, 200mM MgCl2, 28% (w/v) PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.9 Å / Num. obs: 109340 / Rmerge(I) obs: 0.055 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 9.7 |
-Processing
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Refinement | Method to determine structure: SIR, SAD / Resolution: 1.8→19.9 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.863 / SU B: 3.825 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.084 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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