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Open data
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Basic information
Entry | Database: PDB / ID: 5yhx | ||||||||||||
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Title | Structure of Lactococcus lactis ZitR, wild type | ||||||||||||
![]() | Zinc transport transcriptional regulator | ||||||||||||
![]() | METAL BINDING PROTEIN / Zinc binding protein / MarR family / winged Helix-turn-helix / Transcriptional regulator | ||||||||||||
Function / homology | ![]() DNA-binding transcription factor activity / DNA binding / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Song, Y. / Liu, H. / Zhu, R. / Yi, C. / Chen, P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.7 KB | Display | ![]() |
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PDB format | ![]() | 187.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6 MB | Display | ![]() |
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Full document | ![]() | 6 MB | Display | |
Data in XML | ![]() | 40.7 KB | Display | |
Data in CIF | ![]() | 56.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yhyC ![]() 5yhzC ![]() 5yi0C ![]() 5yi1C ![]() 5yi2C ![]() 5yi3C ![]() 3tgnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: IL1403 / Gene: zitR, L168265 / Plasmid: pET28b / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 30%(v/v) Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2012 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→50 Å / Num. obs: 57242 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.31→2.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 2 / Num. unique obs: 2795 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TGN Resolution: 2.4→48.665 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.82 / 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: 40.805 Å2 / ksol: 0.314 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→48.665 Å
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Refine LS restraints |
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LS refinement shell |
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