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Yorodumi- PDB-5yi2: Structure of Lactococcus lactis ZitR, wild type in complex with DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yi2 | ||||||||||||
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Title | Structure of Lactococcus lactis ZitR, wild type in complex with DNA | ||||||||||||
Components |
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Keywords | METAL BINDING PROTEIN / Zinc binding protein / MarR family / winged Helix-turn-helix / Transcriptional regulator | ||||||||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / DNA binding / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) Lactococcus lactis (lactic acid bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Song, Y. / Liu, H. / Zhu, R. / Yi, C. / Chen, P. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2017 Title: Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation. Authors: Zhu, R. / Song, Y. / Liu, H. / Yang, Y. / Wang, S. / Yi, C. / Chen, P.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yi2.cif.gz | 315.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yi2.ent.gz | 248.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yi2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/5yi2 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/5yi2 | HTTPS FTP |
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-Related structure data
Related structure data | 5yhxC 5yhyC 5yhzC 5yi0C 5yi1C 5yi3C 3q5fS 5dmt 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 16445.750 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Strain: IL1403 / Gene: zitR, L168265 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9CDU5 #2: DNA chain | Mass: 4896.215 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Lactococcus lactis (lactic acid bacteria) #3: Chemical | ChemComp-ZN / #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: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 0.1M Sodium cacodylate pH 6.1, 0.05M Magnesium chloride hexahydrate, 0.1M Sodium chloride, 20%(w/v) Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→50 Å / Num. obs: 64593 / % possible obs: 98.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.44→2.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2 / Num. unique obs: 1463 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DMT, 3Q5F Resolution: 2.6→40.116 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.175 Å2 / ksol: 0.306 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→40.116 Å
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Refine LS restraints |
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LS refinement shell |
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