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Yorodumi- PDB-5yi3: Structure of Lactococcus lactis ZitR, C30S mutant in complex with DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yi3 | ||||||||||||
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Title | Structure of Lactococcus lactis ZitR, C30S mutant in complex with DNA | ||||||||||||
Components |
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Keywords | METAL BINDING PROTEIN/DNA / Zinc binding protein / MarR family / winged Helix-turn-helix / Transcriptional regulator / METAL BINDING PROTEIN-DNA complex | ||||||||||||
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: 2.9 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 | 5yi3.cif.gz | 305.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yi3.ent.gz | 239.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yi3_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 5yi3_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5yi3_validation.xml.gz | 49 KB | Display | |
Data in CIF | 5yi3_validation.cif.gz | 66.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/5yi3 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/5yi3 | HTTPS FTP |
-Related structure data
Related structure data | 5yhxC 5yhyC 5yhzC 5yi0C 5yi1C 5yi2C 3q5fS 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 16429.686 Da / Num. of mol.: 8 / Mutation: C30S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (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: 2.83 Å3/Da / Density % sol: 56.5 % |
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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: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2015 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→50 Å / Num. obs: 47584 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.77→2.87 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4718 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q5F Resolution: 2.9→42.486 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.994 Å2 / ksol: 0.299 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.9→42.486 Å
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Refine LS restraints |
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LS refinement shell |
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