+Open data
-Basic information
Entry | Database: PDB / ID: 5z50 | |||||||||
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Title | Crystal structure of PaCysB regulatory domain | |||||||||
Components | Cys regulon transcriptional activator | |||||||||
Keywords | DNA BINDING PROTEIN / CysB / DNA complex | |||||||||
Function / homology | Function and homology information cysteine biosynthetic process / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 Å | |||||||||
Authors | Yang, C. / Liang, H. / Gan, J. | |||||||||
Funding support | China, 2items
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Citation | Journal: Mol.Microbiol. / Year: 2019 Title: Molecular insights into the master regulator CysB-mediated bacterial virulence in Pseudomonas aeruginosa. Authors: Song, Y. / Yang, C. / Chen, G. / Zhang, Y. / Seng, Z. / Cai, Z. / Zhang, C. / Yang, L. / Gan, J. / Liang, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z50.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z50.ent.gz | 156.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/5z50 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/5z50 | HTTPS FTP |
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-Related structure data
Related structure data | 5z4yC 5z4zC 1ixcS 5z4x 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: 26279.482 Da / Num. of mol.: 2 / Fragment: UNP residues 88-324 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O05926 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: 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: 2.66 Å3/Da / Density % sol: 53.83 % Description: the entry contains friedel pairs in F_Plus/minus columns. |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1M MES PH 6.6, 1.6M Ammonium sulfate ,10% 1,4-Dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9725 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9725 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 29819 / % possible obs: 99.8 % / Redundancy: 16.7 % / Rsym value: 0.122 / Net I/σ(I): 18.75 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.523 / Rsym value: 0.414 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IXC Resolution: 2.206→29.39 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 21.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.206→29.39 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 2.1433 Å / Origin y: -18.7042 Å / Origin z: -34.5134 Å
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Refinement TLS group | Selection details: all |