+Open data
-Basic information
Entry | Database: PDB / ID: 5y6i | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa HmgR | ||||||
Components | Transcriptional regulator KdgR | ||||||
Keywords | TRANSCRIPTION / Pseudomonas aeruginosa / HmgR / Quorum sensing | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.517 Å | ||||||
Authors | Gu, T. / Ji, Q. / Liang, H. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Pseudomonas aeruginosa HmgR Authors: Gu, T. / Ji, Q. / Liang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y6i.cif.gz | 189.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y6i.ent.gz | 154.8 KB | Display | PDB format |
PDBx/mmJSON format | 5y6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y6i_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 5y6i_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 5y6i_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 5y6i_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/5y6i ftp://data.pdbj.org/pub/pdb/validation_reports/y6/5y6i | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28009.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: kdgR_2, AOY09_03044, PAERUG_P32_London_17_VIM_2_10_11_04319 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C7CSB5, UniProt: Q9I2A1*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: 2.52 Å3/Da / Density % sol: 51.24 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium citrate tribasic dehydrate, 20% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 19620 / % possible obs: 99 % / Redundancy: 12.8 % / Net I/σ(I): 27.2 |
-Processing
Software |
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Refinement | Resolution: 2.517→48.178 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 34.51 / 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: 2.517→48.178 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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