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Yorodumi- PDB-1xov: The crystal structure of the listeria monocytogenes bacteriophage... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xov | ||||||
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Title | The crystal structure of the listeria monocytogenes bacteriophage PSA endolysin PlyPSA | ||||||
Components | Ply protein | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / multi-domain | ||||||
Function / homology | Function and homology information N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / helicase activity / methyltransferase activity / methylation / metal ion binding Similarity search - Function | ||||||
Biological species | Listeria phage PSA (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Korndoerfer, I.P. / Skerra, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: The crystal structure of the bacteriophage PSA endolysin reveals a unique fold responsible for specific recognition of Listeria cell walls Authors: Korndoerfer, I.P. / Danzer, J. / Schmelcher, M. / Zimmer, M. / Skerra, A. / Loessner, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xov.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xov.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/1xov ftp://data.pdbj.org/pub/pdb/validation_reports/xo/1xov | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36645.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria phage PSA (virus) / Species: Listeria phage 2389 / Description: host: Listeria monocytogenes / Gene: ply / Plasmid: psplpsa / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 References: UniProt: Q8W5Y8, N-acetylmuramoyl-L-alanine amidase |
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-Non-polymers , 7 types, 313 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-GLU / |
#6: Chemical | ChemComp-LYS / |
#7: Chemical | ChemComp-TRS / |
#8: Water | ChemComp-HOH / |
-Details
Nonpolymer details | RESIDUES GLU 2001 AND LYS 2002 ARE UNIDENTIFIED COPURIFIED PEPTIDE. THIS PEPTIDE IS POSSIBLY ...RESIDUES GLU 2001 AND LYS 2002 ARE UNIDENTIFI |
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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: 3.5 Å3/Da / Density % sol: 64.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 100mM hepes, 0.2M (nh4)2so4, 25% peg 3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.92 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 2, 2004 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 48970 / Num. obs: 48940 / % possible obs: 99.92 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 18.79 % / Biso Wilson estimate: 27.08 Å2 / Rsym value: 0.08 / Net I/σ(I): 5.34 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 17 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.05 / Num. unique all: 7005 / Rsym value: 0.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.791 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The data used for refinement is from a native crystal which was only measured a 0.92 A.
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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: 30.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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