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Yorodumi- PDB-4uqy: Coevolution of the ATPase ClpV, the TssB-TssC Sheath and the Acce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uqy | ||||||
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Title | Coevolution of the ATPase ClpV, the TssB-TssC Sheath and the Accessory HsiE Protein Distinguishes Two Type VI Secretion Classes | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / SECRETION / SHEATH / DISASSEMBLY / REGULATION / BACTERIAL | ||||||
Function / homology | Function and homology information Type VI secretion system accessory component TagJ / ImpE protein / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Forster, A. / Planamente, S. / Manoli, E. / Lossi, N.S. / Freemont, P.S. / Filloux, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Coevolution of the ATPase Clpv, the Sheath Proteins Tssb and Tssc and the Accessory Protein Tagj/Hsie1 Distinguishes Type Vi Secretion Classes. Authors: Forster, A. / Planamente, S. / Manoli, E. / Lossi, N.S. / Freemont, P.S. / Filloux, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uqy.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uqy.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uqy_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 4uqy_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 4uqy_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 4uqy_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/4uqy ftp://data.pdbj.org/pub/pdb/validation_reports/uq/4uqy | HTTPS FTP |
-Related structure data
Related structure data | 4uqwC 4uqxC 4uqzC 1zbpS 4uqn C: citing same article (ref.) 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: 28665.506 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / References: UniProt: Q9I746 |
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#2: Protein/peptide | Mass: 2239.558 Da / Num. of mol.: 1 / Fragment: N TERMINUS, RESIDUES 1-20 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / References: UniProt: Q9I749 |
#3: 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: 2.14 Å3/Da / Density % sol: 42.59 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 50 MM MES (PH 6.5) 100 MM AMMONIUM ACETATE 10% GLYCEROL 28% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 |
Detector | Type: ADSC ADSC CCD / Detector: CCD / Date: Feb 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→53 Å / Num. obs: 36309 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.2 % / Biso Wilson estimate: 18.08 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZBP Resolution: 1.6→30.298 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 20.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30.298 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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