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Yorodumi- PDB-5exs: AAA+ ATPase FleQ from Pseudomonas aeruginosa bound to ATP-gamma-S -
+Open data
-Basic information
Entry | Database: PDB / ID: 5exs | ||||||
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Title | AAA+ ATPase FleQ from Pseudomonas aeruginosa bound to ATP-gamma-S | ||||||
Components | Transcriptional regulator FleQ | ||||||
Keywords | TRANSCRIPTION / Transcription factor / AAA+ / ATPase / c-di-GMP | ||||||
Function / homology | Function and homology information positive regulation of cilium-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / cyclic-di-GMP binding / negative regulation of extracellular matrix assembly / positive regulation of cell-substrate adhesion / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding ...positive regulation of cilium-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / cyclic-di-GMP binding / negative regulation of extracellular matrix assembly / positive regulation of cell-substrate adhesion / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Navarro, M.V.A.S. / Sondermann, H. / Matsuyama, B. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Mechanistic insights into c-di-GMP-dependent control of the biofilm regulator FleQ from Pseudomonas aeruginosa. Authors: Matsuyama, B.Y. / Krasteva, P.V. / Baraquet, C. / Harwood, C.S. / Sondermann, H. / Navarro, M.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5exs.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5exs.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 5exs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5exs_validation.pdf.gz | 727.2 KB | Display | wwPDB validaton report |
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Full document | 5exs_full_validation.pdf.gz | 731.3 KB | Display | |
Data in XML | 5exs_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 5exs_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/5exs ftp://data.pdbj.org/pub/pdb/validation_reports/ex/5exs | HTTPS FTP |
-Related structure data
Related structure data | 5expSC 5extC 5exxC 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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Unit cell |
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Symmetry | Helical symmetry: (Num. of operations: 5 / Rise per n subunits: 0.2 Å / Rotation per n subunits: 60 °) |
-Components
#1: Protein | Mass: 29300.684 Da / Num. of mol.: 1 / Fragment: UNP residues 137-394 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fleQ, PA1097 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G3XCV0 |
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#2: Chemical | ChemComp-AGS / |
#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: 2.34 Å3/Da / Density % sol: 47.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium sulfate and 25% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→52.6 Å / Num. obs: 9612 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1042 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EXP Resolution: 2.5→52.576 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.17 / 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 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→52.576 Å
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Refine LS restraints |
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LS refinement shell |
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