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Open data
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Basic information
Entry | Database: PDB / ID: 7b1v | |||||||||
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Title | DtxR-like iron-dependent regulator IdeR complexed with cobalt | |||||||||
![]() | DtxR family iron (Metal) dependent repressor | |||||||||
![]() | TRANSCRIPTION / TRANSCRIPTION REGULATION / REPRESSOR / REGULATOR / TRANSCRIPTION REGULATOR / METAL SENSOR / IDER / IRON-DEPENDENT REGULATOR / DTXR / HELIX-TURN-HELIX / METAL ION / METAL-BINDING PROTEIN / DNA BINDING | |||||||||
Function / homology | ![]() transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Maurer, D. / Marcos-Torres, F.J. / Griese, J.J. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.2 KB | Display | ![]() |
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PDB format | ![]() | 74.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 365.1 KB | Display | ![]() |
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Full document | ![]() | 365.1 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b1yC ![]() 7b20C ![]() 7b23C ![]() 7b24C ![]() 7b25C ![]() 1u8rS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25676.365 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338 Gene: A8924_2181 / Plasmid: pET-28a(+) / Production host: ![]() ![]() #2: Chemical | ChemComp-CO / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 25%(w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→61.1 Å / Num. obs: 17216 / % possible obs: 83.5 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.037 / Rrim(I) all: 0.069 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.04→2.22 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 862 / CC1/2: 0.658 / Rpim(I) all: 0.465 / Rrim(I) all: 0.748 / % possible all: 54.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1U8R Resolution: 2.04→61.1 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.051 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.677 / ESU R Free: 0.293 / 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: 87.01 Å2 / Biso mean: 35.79 Å2 / Biso min: 17.75 Å2
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Refinement step | Cycle: final / Resolution: 2.04→61.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.043→2.096 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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