+Open data
-Basic information
Entry | Database: PDB / ID: 4n58 | ||||||
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Title | Crystal Structure of Pectocin M2 at 1.86 Angstroms | ||||||
Components | Pectocin M2 | ||||||
Keywords | HYDROLASE / Plant-Like ferredoxin / Colicin M-like cytotoxic domain / Lipid-II hydrolase / Bacteriocin / Protein Antibiotc | ||||||
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 PBR1692 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å | ||||||
Authors | Grinter, R. / Roszak, A.W. / Zeth, K. / Cogdell, C.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 | 4n58.cif.gz | 243.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n58.ent.gz | 198.7 KB | Display | PDB format |
PDBx/mmJSON format | 4n58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/4n58 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/4n58 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#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 PBR1692 (bacteria) Strain: PBR1692 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A0A067XG75*PLUS |
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-Non-polymers , 6 types, 504 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MPD / ( #6: Chemical | ChemComp-CL / | #7: 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: 4.14 Å3/Da / Density % sol: 70.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.8 M Ammonium Sulphate, 3% MPD, 0.1 M MES, 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: Diamond / Beamline: I02 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2012 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→64.22 Å / Num. all: 86224 / Num. obs: 86224 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 20 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 47 |
Reflection shell | Resolution: 1.86→1.91 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 5.5 / Num. unique all: 6313 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.86→58.79 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.72 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / 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: 47.237 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→58.79 Å
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Refine LS restraints |
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