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Yorodumi- PDB-7b20: DtxR-like iron-dependent regulator IdeR complexed with iron and i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b20 | ||||||||||||
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Title | DtxR-like iron-dependent regulator IdeR complexed with iron and its consensus DNA-binding sequence | ||||||||||||
Components |
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Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION / REPRESSOR / REGULATOR / TRANSCRIPTION REGULATOR / METAL SENSOR / IDER / IRON-DEPENDENT REGULATOR / DTXR / HELIX-TURN-HELIX / METAL ION / METAL-BINDING PROTEIN / DNA BINDING / PROTEIN-DNA COMPLEX | ||||||||||||
Function / homology | Function and homology information transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharopolyspora erythraea (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||||||||
Authors | Maurer, D. / Marcos-Torres, F.J. / Griese, J.J. | ||||||||||||
Funding support | Sweden, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout. Authors: Marcos-Torres, F.J. / Maurer, D. / Juniar, L. / Griese, J.J. #1: Journal: Biorxiv / Year: 2021 Title: The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout Authors: Marcos-Torres, F.J. / Maurer, D. / Griese, J.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b20.cif.gz | 229 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b20.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7b20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/7b20 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/7b20 | HTTPS FTP |
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-Related structure data
Related structure data | 7b1vSC 7b1yC 7b23C 7b24C 7b25C S: Starting model for refinement C: citing same article (ref.) |
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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: 25644.367 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: There is a domain swap with symmetry mates. The C-terminal domains associated with chains A and D originate from chains D and A of a symmetry mate, respectively, and have therefore been ...Details: There is a domain swap with symmetry mates. The C-terminal domains associated with chains A and D originate from chains D and A of a symmetry mate, respectively, and have therefore been named chains dd and aa. The swap is only possible for chains A and D, but not for chains B and C, due to crystal packing interactions. Source: (gene. exp.) Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338) (bacteria) Strain: ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338 Gene: A8924_2181 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2A9J1W2 #2: DNA chain | | Mass: 9222.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide / Source: (synth.) synthetic construct (others) / References: UniProt: A0A2A9J1W2*PLUS #3: DNA chain | | Mass: 9222.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-FE2 / #5: Water | ChemComp-HOH / | Compound details | There is a domain swap with symmetry mates. The C-terminal domains associated with chains A and D ...There is a domain swap with symmetry mates. The C-terminal domains associated with chains A and D originate from chains D and A of a symmetry mate, respectively, and have therefore been named chains dd and aa. The swap is only possible for chains A and D, but not for chains B and C, due to crystal packing interactions. | Has ligand of interest | Y | |
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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: 3.55 Å3/Da / Density % sol: 65.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30%(w/v) PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97624 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→54.29 Å / Num. obs: 54157 / % possible obs: 91.1 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.18→2.44 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2708 / CC1/2: 0.516 / Rpim(I) all: 0.463 / Rrim(I) all: 1.229 / % possible all: 59.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7B1V Resolution: 2.18→54.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.513 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.02 Å2 / Biso mean: 57.867 Å2 / Biso min: 31.75 Å2
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Refinement step | Cycle: final / Resolution: 2.18→54.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.181→2.237 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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