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Open data
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Basic information
Entry | Database: PDB / ID: 5yi0 | ||||||||||||
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Title | Structure of Lactococcus lactis ZitR, C30AH42A mutant | ||||||||||||
![]() | 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 | ![]() | 127.1 KB | Display | ![]() |
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PDB format | ![]() | 99 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yhxC ![]() 5yhySC ![]() 5yhzC ![]() 5yi1C ![]() 5yi2C ![]() 5yi3C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16346.614 Da / Num. of mol.: 4 / Mutation: C30A H42A 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: 3.66 Å3/Da / Density % sol: 66.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 42%(v/v) Polyethylene glycol 200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2013 |
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: 2.15→50 Å / Num. obs: 49739 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2585 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YHY Resolution: 2.3→19.549 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.949 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.549 Å
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Refine LS restraints |
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LS refinement shell |
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