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Yorodumi- PDB-4fzn: Crystal structure of syringacin M mutant D232A from Pseudomonas s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fzn | ||||||
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Title | Crystal structure of syringacin M mutant D232A from Pseudomonas syringae pv. tomato DC3000 | ||||||
Components | Bacteriocin | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Phosphatase | ||||||
Function / homology | Function and homology information killing of cells of another organism / defense response to bacterium / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas syringae pv. tomato (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å | ||||||
Authors | Roszak, A.W. / Grinter, R. / Cogdell, J.R. / Walker, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: The Crystal Structure of the Lipid II-degrading Bacteriocin Syringacin M Suggests Unexpected Evolutionary Relationships between Colicin M-like Bacteriocins. Authors: Grinter, R. / Roszak, A.W. / Cogdell, R.J. / Milner, J.J. / Walker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fzn.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fzn.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 4fzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/4fzn ftp://data.pdbj.org/pub/pdb/validation_reports/fz/4fzn | HTTPS FTP |
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-Related structure data
Related structure data | 4fzlC 4fzmSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30539.068 Da / Num. of mol.: 1 / Mutation: D232A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Strain: DC3000 / Gene: PSPTO_0572 / Plasmid: pETMDC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q88A25 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density % sol: 79.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 7% w/v PEG 8000, 30% v/v ethylene glycol 0.03 M CaCl2, 0.03 M MgCl2, 5% dimethyl sulfoxide, 0.1 M Bicine/Tris base, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.12→40.09 Å / Num. all: 13347 / Num. obs: 13347 / % possible obs: 99.53 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 107.9 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 3.12→3.2 Å / Redundancy: 16.2 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1018 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FZM Resolution: 3.12→40.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 26.446 / SU ML: 0.209 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 98.702 Å2
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Refinement step | Cycle: LAST / Resolution: 3.12→40.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.121→3.201 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -70.2903 Å / Origin y: 16.4942 Å / Origin z: -10.244 Å
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