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Yorodumi- PDB-5yi1: Structure of Lactococcus lactis ZitR, C30AH42A mutant in apo form -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yi1 | ||||||||||||
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Title | Structure of Lactococcus lactis ZitR, C30AH42A mutant in apo form | ||||||||||||
Components | Zinc transport transcriptional regulator | ||||||||||||
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) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 5yi1.cif.gz | 40.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yi1.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 5yi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yi1_validation.pdf.gz | 426.5 KB | Display | wwPDB validaton report |
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Full document | 5yi1_full_validation.pdf.gz | 427.8 KB | Display | |
Data in XML | 5yi1_validation.xml.gz | 7 KB | Display | |
Data in CIF | 5yi1_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/5yi1 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/5yi1 | HTTPS FTP |
-Related structure data
Related structure data | 5yhxC 5yhyC 5yhzC 5yi0SC 5yi2C 5yi3C 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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Unit cell |
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-Components
#1: Protein | Mass: 16346.614 Da / Num. of mol.: 1 / Mutation: C30A, H42A 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 63%(v/v) Polyethylene glycol 200, 10mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2013 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 14987 / % possible obs: 98.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 2.07→2.14 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1463 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YI0 Resolution: 2.2→27.585 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.01 / 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: 59.896 Å2 / ksol: 0.399 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→27.585 Å
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Refine LS restraints |
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LS refinement shell |
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