+Open data
-Basic information
Entry | Database: PDB / ID: 7b0c | ||||||
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Title | [4Fe-4S]-NsrR complexed to 23-bp HmpA1 operator fragment | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / NO SENSOR / IRON SULFUR CLUSTER / TRANSCRIPTION / DNA COMPLEX | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Rohac, R. / Fontecilla-Camps, J.C. / Volbeda, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: Structural determinants of DNA recognition by the NO sensor NsrR and related Rrf2-type [FeS]-transcription factors. Authors: Rohac, R. / Crack, J.C. / de Rosny, E. / Gigarel, O. / Le Brun, N.E. / Fontecilla-Camps, J.C. / Volbeda, A. #1: Journal: Nat Commun / Year: 2017 Title: Crystal structures of the NO sensor NsrR reveal how its iron-sulfur cluster modulates DNA binding. Authors: Volbeda, A. / Dodd, E.L. / Darnault, C. / Crack, J.C. / Renoux, O. / Hutchings, M.I. / Le Brun, N.E. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b0c.cif.gz | 198.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b0c.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 7b0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/7b0c ftp://data.pdbj.org/pub/pdb/validation_reports/b0/7b0c | HTTPS FTP |
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-Related structure data
Related structure data | 5n07S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 17503.107 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: nsrR, SCO7427, SC6D11.23 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L132 #2: DNA chain | | Mass: 6976.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria) #3: DNA chain | | Mass: 7140.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria) #4: Chemical | #5: Water | ChemComp-HOH / | 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: 3.72 Å3/Da / Density % sol: 66.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 550 MME, PEG 20000, magnesium chloride, calcium chloride, MOPS/HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 3→67.54 Å / Num. obs: 14398 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 131.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3→3.18 Å / Rmerge(I) obs: 1.9 / Num. unique obs: 2320 / CC1/2: 0.332 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N07 Resolution: 3→51.45 Å / SU ML: 0.5348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.624 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: 148.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→51.45 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.28779804623 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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