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Yorodumi- PDB-6fi9: Crystal Structure of a zinc-responsive MarR family member, Lactoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fi9 | ||||||
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Title | Crystal Structure of a zinc-responsive MarR family member, Lactococcus lactis ZitR | ||||||
Components | Transcriptional regulator ZitR | ||||||
Keywords | GENE REGULATION / Zinc transport Regulator / Adhesin competence Regulator / Multiple antibiotic resistance Regulator / Zinc Responsive Repressor / winged Helix-Turn-Helix DNA binding domain | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Lactococcus lactis subsp. cremoris (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Varela, P.F. / Legrand, P. | ||||||
Funding support | France, 1items
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Citation | Journal: PLoS ONE / Year: 2019 Title: Biophysical and structural characterization of a zinc-responsive repressor of the MarR superfamily. Authors: Varela, P.F. / Velours, C. / Aumont-Nicaise, M. / Pineau, B. / Legrand, P. / Poquet, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fi9.cif.gz | 469.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fi9.ent.gz | 394.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fi9_validation.pdf.gz | 486.6 KB | Display | wwPDB validaton report |
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Full document | 6fi9_full_validation.pdf.gz | 512.5 KB | Display | |
Data in XML | 6fi9_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 6fi9_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/6fi9 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/6fi9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16307.568 Da / Num. of mol.: 8 / Mutation: S2A, A4R, D8E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria) Strain: MG1363 / Gene: zitR, llmg_2401 / Plasmid: pVE8073 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2RNS2 #2: Chemical | ChemComp-ZN / |
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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: 2.78 Å3/Da / Density % sol: 55.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M sodium citrate tribasic dihydrate 30 % polyethyleneglycol 4.000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28189 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28189 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→48.11 Å / Num. obs: 26339 / % possible obs: 99.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 102.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06722 / Rrim(I) all: 0.09506 / Net I/av σ(I): 12.7 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 3.09→3.17 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1860 / CC1/2: 0.597 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→48.15 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.516
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Displacement parameters | Biso max: 300 Å2 / Biso mean: 162.16 Å2 / Biso min: 46.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.58 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→48.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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