+Open data
-Basic information
Entry | Database: PDB / ID: 4n59 | ||||||
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Title | The Crystal Structure of Pectocin M2 at 2.3 Angstroms | ||||||
Components | Pectocin M2 | ||||||
Keywords | HYDROLASE / Lipid-II Hydrolase / Bacteriocin / Protein Antibiotic | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / electron transfer activity / defense response to bacterium / metal ion binding Similarity search - Function | ||||||
Biological species | Pectobacterium carotovorum subsp. brasiliensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Zeth, K. / Grinter, R. / Roszak, A.W. / Cogdell, R.J. / Walker, D. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2014 Title: Structure of the atypical bacteriocin pectocin M2 implies a novel mechanism of protein uptake. Authors: Grinter, R. / Josts, I. / Zeth, K. / Roszak, A.W. / McCaughey, L.C. / Cogdell, R.J. / Milner, J.J. / Kelly, S.M. / Byron, O. / Walker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n59.cif.gz | 217.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n59.ent.gz | 177 KB | Display | PDB format |
PDBx/mmJSON format | 4n59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/4n59 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/4n59 | HTTPS FTP |
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-Related structure data
Related structure data | 4n58SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30903.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium carotovorum subsp. brasiliensis (bacteria) Strain: PBR1692 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A0A067XG75*PLUS #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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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: 2.55 Å3/Da / Density % sol: 51.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15 % PEG3350, 0.2 M Ammonium sulphate, 3% MPD, 0.1M Bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2012 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 55667 / Num. obs: 52652 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.41 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.85 / % possible all: 95.7 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: pdb entry 4N58 Resolution: 2.3→44.52 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.992 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.256 / 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: 67.992 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→44.52 Å
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Refine LS restraints |
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