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Yorodumi- PDB-7erq: The regulatory domain of YeiE, a sulfite sensing LysR-type transc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7erq | ||||||
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Title | The regulatory domain of YeiE, a sulfite sensing LysR-type transcriptional regulator from Cronobacter sakazakii (ligand-free form) | ||||||
Components | LysR family transcriptional regulator | ||||||
Keywords | DNA BINDING PROTEIN / LysR-type transcriptional regulator / LTTR / Cronobacter sakazakii / sulfite | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Cronobacter sakazakii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Hong, S. / Ha, N.-C. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Crystal structures of YeiE from Cronobacter sakazakii and the role of sulfite tolerance in gram-negative bacteria. Authors: Hong, S. / Kim, J. / Cho, E. / Na, S. / Yoo, Y.J. / Cho, Y.H. / Ryu, S. / Ha, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7erq.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7erq.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 7erq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/7erq ftp://data.pdbj.org/pub/pdb/validation_reports/er/7erq | HTTPS FTP |
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-Related structure data
Related structure data | 7erpSC 7fdfC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23279.971 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cronobacter sakazakii (bacteria) / Gene: YeiE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H9BVC9 #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop Details: 0.1M Hydroxyethyl piperazineetahnesulfonic acid (HEPES) pH 7.5, 11% (v/v) PEG 10000, 6% (v/v) 2-Methyl-2,4-pentanediol (MPD), 50microM sodium selenite |
-Data collection
Diffraction | Mean temperature: 100.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 35724 / % possible obs: 99.1 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.58 Å2 / CC star: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.018 / Net I/σ(I): 28.17 |
Reflection shell | Resolution: 1.95→1.98 Å / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.54 / Num. unique obs: 1625 / CC star: 0.845 / Rpim(I) all: 0.161 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ERP Resolution: 1.95→49.28 Å / SU ML: 0.212 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 22.3939 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→49.28 Å
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Refine LS restraints |
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LS refinement shell |
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