+Open data
-Basic information
Entry | Database: PDB / ID: 5z4z | ||||||
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Title | Crystal structure of PaCysB NTD domain with space group C2 | ||||||
Components | Transcriptional regulator CysB | ||||||
Keywords | DNA BINDING PROTEIN / CysB | ||||||
Function / homology | Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 Å | ||||||
Authors | Yang, C. / Liang, H. / Gan, J. | ||||||
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 | 5z4z.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z4z.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 5z4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/5z4z ftp://data.pdbj.org/pub/pdb/validation_reports/z4/5z4z | HTTPS FTP |
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-Related structure data
Related structure data | 5z4yC 5z50C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10312.711 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET28SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2C6M5K9 #2: Chemical | ChemComp-SO4 / | #3: 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: 2.65 Å3/Da / Density % sol: 53.65 % Description: the entry contains friedel pairs in F-plus/minus columns |
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Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop Details: 10% 2-propanol,0.1M sodium phosphate/citric acid PH4.2 0.2M lithium sulfate |
-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: Dec 24, 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: 2.05→30 Å / Num. obs: 18944 / % possible obs: 94.2 % / Redundancy: 4.1 % / Rsym value: 0.118 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.376 / Rsym value: 0.309 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IXC Resolution: 2.053→29.444 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 25.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.053→29.444 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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