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- PDB-6y42: Crystal Structure of RsrR complexed to a 39 basepair DNA fragment... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y42 | |||||||||
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Title | Crystal Structure of RsrR complexed to a 39 basepair DNA fragment of the rsrR promoter | |||||||||
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Function / homology | ![]() Transcription regulator Rrf2-type, conserved site / Rrf2-type HTH domain signature. / Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily Similarity search - Domain/homology | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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 | ![]() | 113.7 KB | Display | ![]() |
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PDB format | ![]() | 82.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6y45C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 17385.975 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SVEN_6563 / Plasmid: pGS-21a / Cell line (production host): BL21(DE3) Production host: ![]() ![]() ![]() References: UniProt: F2RGC9 #2: DNA chain | | Mass: 12127.805 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() #3: DNA chain | | Mass: 11878.648 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() #4: Chemical | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.86 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion Details: NaCl, MgCl2, CaCl2, PEG1000, PEG3350, MES, anaerobic (in glove box) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 4.3→49.34 Å / Num. obs: 6038 / % possible obs: 99.5 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.057 / Rrim(I) all: 0.104 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 4.3→4.45 Å / Rmerge(I) obs: 2.13 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3563 / CC1/2: 0.36 / Rpim(I) all: 0.988 / Rrim(I) all: 2.53 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6hsd Resolution: 4.3→49.34 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.939 / SU B: 132.744 / SU ML: 1.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.077 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: 387.16 Å2 / Biso mean: 253.122 Å2 / Biso min: 185.85 Å2
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Refinement step | Cycle: final / Resolution: 4.3→49.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.3→4.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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