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Yorodumi- PDB-4ru3: Crystal structure of the cell puncturing protein Orf41 from Pseud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ru3 | ||||||
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Title | Crystal structure of the cell puncturing protein Orf41 from Pseudomonas phage SN | ||||||
Components | puncturing protein gp41 | ||||||
Keywords | CELL INVASION / gp41 / membrane translocation / phage baseplate / Cell puncturing device | ||||||
Function / homology | Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Vgr protein, OB-fold domain superfamily / metal ion binding / : / Putative baseplate protein Function and homology information | ||||||
Biological species | Pseudomonas phage SN (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.172 Å | ||||||
Authors | Browning, C. / Shneider, M.M. / Leiman, P.G. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the cell puncturing protein Orf41 from Pseudomonas phage SN Authors: Browning, C. / Shneider, M.M. / Leiman, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ru3.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ru3.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ru3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/4ru3 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/4ru3 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24085.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage SN (virus) / Gene: ORF41 Plasmid: pEE3, pET-23 derivative (TEV cleavage site after His-tag) Production host: Escherichia coli (E. coli) / Strain (production host): B834/DE3 / References: UniProt: B7VFI6 |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.09 Å3/Da / Density % sol: 41.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5 Details: 21% PEG 10K, 0.1M Ammonium acetate, 0.1M Bis-Tris pH 5.0, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2011 |
Radiation | Monochromator: Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→34.513 Å / Num. all: 67585 / Num. obs: 67579 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 17.7 % / Rmerge(I) obs: 0.068 / Rsym value: 0.071 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.17→1.24 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 8.8 / Num. unique all: 9781 / Rsym value: 0.309 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.172→34.513 Å / SU ML: 0.07 / σ(F): 0.08 / Phase error: 11.31 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.172→34.513 Å
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Refine LS restraints |
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LS refinement shell |
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