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Yorodumi- PDB-4led: The Crystal Structure of Pyocin L1 bound to D-rhamnose at 2.37 An... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4led | ||||||
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Title | The Crystal Structure of Pyocin L1 bound to D-rhamnose at 2.37 Angstroms | ||||||
Components | Pyocin L1 | ||||||
Keywords | SUGAR BINDING PROTEIN / Monocot Mannose Binding Protein / Galanthus nivalis agglutinin / Beta Prism / Bacteriocin / Antimicrobial Protein / Extracellular | ||||||
Function / homology | Function and homology information Agglutinin, subunit A - #30 / Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||
Authors | Grinter, R. / Roszak, A.W. / Mccaughey, L. / Cogdell, C.J. / Walker, D. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014 Title: Lectin-Like Bacteriocins from Pseudomonas spp. Utilise D-Rhamnose Containing Lipopolysaccharide as a Cellular Receptor. Authors: McCaughey, L.C. / Grinter, R. / Josts, I. / Roszak, A.W. / Walen, K.I. / Cogdell, R.J. / Milner, J. / Evans, T. / Kelly, S. / Tucker, N.P. / Byron, O. / Smith, B. / Walker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4led.cif.gz | 211.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4led.ent.gz | 172.5 KB | Display | PDB format |
PDBx/mmJSON format | 4led.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4led_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 4led_full_validation.pdf.gz | 468.6 KB | Display | |
Data in XML | 4led_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 4led_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/4led ftp://data.pdbj.org/pub/pdb/validation_reports/le/4led | HTTPS FTP |
-Related structure data
Related structure data | 4le7SC 4leaC 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30008.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: C 1433 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: T2LG16*PLUS #2: Sugar | ChemComp-XXR / #3: 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: 2.67 Å3/Da / Density % sol: 53.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 550 MME, 20% PEG 20K, 0.03 M CaCl2, 0.03 M MgCl2 0.1 M MOPS/HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9788 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→54.93 Å / Num. obs: 26242 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 43.618 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.37→2.43 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1922 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LE7 Resolution: 2.37→54.93 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.595 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.362 / ESU R Free: 0.255 / 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: 54.163 Å2
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Refinement step | Cycle: LAST / Resolution: 2.37→54.93 Å
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Refine LS restraints |
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