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- PDB-4fzn: Crystal structure of syringacin M mutant D232A from Pseudomonas s... -
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Open data
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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 | ||||||
![]() | Bacteriocin | ||||||
![]() | ANTIMICROBIAL PROTEIN / Phosphatase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roszak, A.W. / Grinter, R. / Cogdell, J.R. / Walker, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.6 KB | Display | ![]() |
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PDB format | ![]() | 97.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431 KB | Display | ![]() |
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Full document | ![]() | 436 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fzlC ![]() 4fzmSC C: citing same article ( S: Starting model for refinement |
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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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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.) ![]() Strain: DC3000 / Gene: PSPTO_0572 / Plasmid: pETMDC / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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