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Yorodumi- PDB-4b62: The structure of the cell wall anchor of the T6SS from Pseudomona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b62 | ||||||
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Title | The structure of the cell wall anchor of the T6SS from Pseudomonas aeruginosa | ||||||
Components | TSSL1 | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Robb, C.S. / Carlson, M. / Nano, F.E. / Boraston, A.B. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Periplasmic Peptidoglycan Binding Anchor of a T6Ss from Pseudomonas Aeruginosa. Authors: Robb, C.S. / Carlson, M. / Nano, F.E. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b62.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b62.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 4b62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/4b62 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/4b62 | HTTPS FTP |
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-Related structure data
Related structure data | 3khnS 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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Unit cell |
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-Components
#1: Protein | Mass: 17076.113 Da / Num. of mol.: 1 / Fragment: PEPTIDOGLYCAN BINDING MODULE, RESIDUES 299-449 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I754 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 34 % / Description: NONE |
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Crystal grow | pH: 6.9 / Details: SODIUM/POTASSIUM PHOSPHATE PH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 1, 2011 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→21.83 Å / Num. obs: 22823 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.45→1.52 Å / Redundancy: 3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.4 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KHN Resolution: 1.45→21.84 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.801 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 15.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→21.84 Å
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Refine LS restraints |
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