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Yorodumi- PDB-5nl9: Crystal structure of a peroxide stress regulator from Leptospira ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nl9 | ||||||
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Title | Crystal structure of a peroxide stress regulator from Leptospira interrogans | ||||||
Components | Transcriptional regulator (FUR family) | ||||||
Keywords | DNA BINDING PROTEIN / Leptospira / oxidative stress response / Fur family / asymmetric homodimer | ||||||
Function / homology | Ferric-uptake regulator / Ferric uptake regulator family / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / : / Transcriptional regulator (FUR family) Function and homology information | ||||||
Biological species | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Saul, F.A. / Haouz, A. / Picardeau, M. / Benaroudj, N. | ||||||
Funding support | France, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structure and function of the Leptospira interrogans peroxide stress regulator (PerR), an atypical PerR devoid of a structural metal-binding site. Authors: Kebouchi, M. / Saul, F. / Taher, R. / Landier, A. / Beaudeau, B. / Dubrac, S. / Weber, P. / Haouz, A. / Picardeau, M. / Benaroudj, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nl9.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nl9.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/5nl9 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/5nl9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16995.502 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130) (bacteria) Strain: Fiocruz L1-130 / Gene: LIC_12034 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72QS5 #2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | #5: 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: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG-3350, 0.2M potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28215 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28215 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.84 Å / Num. obs: 27475 / % possible obs: 97.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 32.81 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 2.6 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→46.84 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.9278 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.138
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Displacement parameters | Biso mean: 41.34 Å2
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Refine analyze | Luzzati coordinate error obs: 0.273 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→46.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.98 Å / Total num. of bins used: 13
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