+Open data
-Basic information
Entry | Database: PDB / ID: 5xhx | ||||||
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Title | Crystal structure of VqsR LBD domain from Pseudomonas aeruginosa | ||||||
Components | Helix-turn-helix transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / autoinducer transcriptional regulator PAO1 | ||||||
Function / homology | Function and homology information : / positive regulation of secondary metabolite biosynthetic process / phosphorelay response regulator activity / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Gu, L. / He, Q. / Wang, K. / Wang, F. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of VqsR LBD domain from Pseudomonas aeruginosa Authors: Gu, L. / He, Q. / Wang, K. / Wang, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xhx.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xhx.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/5xhx ftp://data.pdbj.org/pub/pdb/validation_reports/xh/5xhx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22374.197 Da / Num. of mol.: 2 / Fragment: UNP residues 1-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: PA2591, nreC_2, nreC, nreC_1, nreC_3, AOY09_03830, BH593_21715, CCBH4851_00420, PAERUG_E15_London_28_01_14_06660, PAERUG_P32_London_17_VIM_2_10_11_00166, PAMH19_6192 Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZQT2, UniProt: Q9I0P6*PLUS #2: Water | ChemComp-HOH / | |
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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: 3.01 Å3/Da / Density % sol: 59.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.01M Magnesium acetate tetrahydrate 0.05M Sodium cacodylate trihydrate pH 6.5 1.3M Lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 32086 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 26.04 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→36.414 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→36.414 Å
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Refine LS restraints |
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LS refinement shell |
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