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Open data
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Basic information
Entry | Database: PDB / ID: 6y45 | |||||||||
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Title | Crystal Structure of the H33A variant of RsrR | |||||||||
![]() | Rrf2 family transcriptional regulator | |||||||||
![]() | TRANSCRIPTION / REDOX SENSOR / IRON SULFUR CLUSTER | |||||||||
Function / homology | ![]() 2 iron, 2 sulfur cluster binding / DNA-binding transcription factor activity / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rohac, R. / Volbeda, A. / Fontecilla-Camps, J.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Electron and Proton Transfers Modulate DNA Binding by the Transcription Regulator RsrR. Authors: Crack, J.C. / Amara, P. / Volbeda, A. / Mouesca, J.M. / Rohac, R. / Pellicer Martinez, M.T. / Huang, C.Y. / Gigarel, O. / Rinaldi, C. / Le Brun, N.E. / Fontecilla-Camps, J.C. #1: ![]() Title: Crystal Structure of the Transcription Regulator RsrR Reveals a [2Fe-2S] Cluster Coordinated by Cys, Glu, and His Residues. Authors: Volbeda, A. / Martinez, M.T.P. / Crack, J.C. / Amara, P. / Gigarel, O. / Munnoch, J.T. / Hutchings, M.I. / Darnault, C. / Le Brun, N.E. / Fontecilla-Camps, J.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 265.7 KB | Display | ![]() |
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PDB format | ![]() | 215.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y42C ![]() 6hsdS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 17318.904 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SVEN_6563 Production host: ![]() ![]() References: UniProt: F2RGC9 |
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-Non-polymers , 6 types, 455 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FES / #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-MES / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 / Details: NaCl, MPD, MES, dithionite, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→45.14 Å / Num. obs: 68787 / % possible obs: 96.5 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.062 / Net I/σ(I): 12.02 |
Reflection shell | Resolution: 1.68→1.78 Å / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 0.67 / Num. unique obs: 10773 / CC1/2: 0.433 / Rrim(I) all: 1.66 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6hsd Resolution: 1.68→45.14 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 6.836 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.1 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.56 Å2 / Biso mean: 37.062 Å2 / Biso min: 22.46 Å2
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Refinement step | Cycle: final / Resolution: 1.68→45.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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