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- PDB-2nuk: Soluble Domain of the Rieske Iron-Sulfur Protein from Rhodobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nuk | ||||||
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Title | Soluble Domain of the Rieske Iron-Sulfur Protein from Rhodobacter sphaeroides | ||||||
![]() | Ubiquinol-cytochrome c reductase iron-sulfur subunit | ||||||
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Function / homology | ![]() quinol-cytochrome-c reductase / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kolling, D. / Brunzelle, J. / Lhee, S. / Crofts, A.R. / Nair, S.K. | ||||||
![]() | ![]() Title: Atomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters. Authors: Kolling, D.J. / Brunzelle, J.S. / Lhee, S. / Crofts, A.R. / Nair, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.4 KB | Display | ![]() |
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PDB format | ![]() | 74.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2numC ![]() 2nveC ![]() 2nvfC ![]() 2nvgC ![]() 2nwfSC C: citing same article ( S: Starting model for refinement |
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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: 15162.142 Da / Num. of mol.: 1 / Fragment: residues 47-187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FES / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.27 % |
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Crystal grow![]() | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.5 M Ammonium sulfate, 20% anhydrous glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.2→12 Å / Num. all: 41254 / Num. obs: 41254 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 19.6 / Num. unique all: 4192 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 2NWF Resolution: 1.2→11.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.669 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.781 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→11.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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