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Yorodumi- PDB-6yhv: Structural insights into Pseudomonas aeruginosa Type six secretio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yhv | ||||||
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Title | Structural insights into Pseudomonas aeruginosa Type six secretion system exported effector 8: unliganded Tse8 | ||||||
Components | Tse8 | ||||||
Keywords | TOXIN / Amidase Signature (AS) superfamily complex | ||||||
Function / homology | Amidase signature domain / Amidase signature (AS) superfamily / Amidase / COPPER (II) ION / Amidase domain-containing protein Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.893 Å | ||||||
Authors | Sainz-Polo, M.A. / Capuni, R. / Pretre, G. / Gonzalez-Magana, A. / Lucas, M. / Altuna, J. / Montanchez, I. / Fucini, P. / Albesa-Jove, D. | ||||||
Funding support | Spain, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Structural insights into Pseudomonas aeruginosaType six secretion system exported effector 8. Authors: Gonzalez-Magana, A. / Sainz-Polo, M.A. / Pretre, G. / Capuni, R. / Lucas, M. / Altuna, J. / Montanchez, I. / Fucini, P. / Albesa-Jove, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yhv.cif.gz | 408 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yhv.ent.gz | 334.3 KB | Display | PDB format |
PDBx/mmJSON format | 6yhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yhv_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 6yhv_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 6yhv_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 6yhv_validation.cif.gz | 63.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/6yhv ftp://data.pdbj.org/pub/pdb/validation_reports/yh/6yhv | HTTPS FTP |
-Related structure data
Related structure data | 6te4SC 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
#1: Protein | Mass: 63517.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 / Gene: PA4163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWL8 #2: Chemical | ChemComp-CU / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.46 Å3/Da / Density % sol: 49.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M calcium acetate, 0.1 M Sodium cacodylate pH 6.5 and 18% PEG8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.893→42.83 Å / Num. obs: 94264 / % possible obs: 93.55 % / Redundancy: 3.5 % / CC1/2: 0.953 / CC star: 0.988 / Net I/σ(I): 5.22 |
Reflection shell | Resolution: 1.893→1.96 Å / Rmerge(I) obs: 1.459 / Num. unique obs: 8315 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TE4 Resolution: 1.893→42.83 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.93 / Phase error: 27.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.893→42.83 Å
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Refine LS restraints |
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LS refinement shell |
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