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Yorodumi- PDB-5his: Crystal Structure of PQS Response Protein PqsE in Complex with 3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5his | ||||||
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Title | Crystal Structure of PQS Response Protein PqsE in Complex with 3-methylthiophene-2-carboxylic acid | ||||||
Components | PqsE | ||||||
Keywords | METAL BINDING PROTEIN / quorum sensing / pqs / pqsE / inhibitor / pseudomonas | ||||||
Function / homology | Function and homology information 2-aminobenzoylacetyl-CoA thioesterase / secondary metabolite biosynthetic process / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.77 Å | ||||||
Authors | Witzgall, F. / Blankenfeldt, W. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Dissecting the Multiple Roles of PqsE in Pseudomonas aeruginosa Virulence by Discovery of Small Tool Compounds. Authors: Zender, M. / Witzgall, F. / Drees, S.L. / Weidel, E. / Maurer, C.K. / Fetzner, S. / Blankenfeldt, W. / Empting, M. / Hartmann, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5his.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5his.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 5his.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5his_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 5his_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 5his_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5his_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/5his ftp://data.pdbj.org/pub/pdb/validation_reports/hi/5his | HTTPS FTP |
-Related structure data
Related structure data | 5hioC 5hipC 5hiqC 2q0iS 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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-Components
#1: Protein | Mass: 34545.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA1000 / Details (production host): pET19m / Production host: Escherichia coli (E. coli) / References: UniProt: P20581 | ||||
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#2: Chemical | #3: Chemical | ChemComp-60P / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES, 200 mM MgCl2, 31% PEG400 / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→48.759 Å / Num. obs: 31806 / % possible obs: 100 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.77→1.81 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2Q0I Resolution: 1.77→48.759 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.27 / 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: 1.77→48.759 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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