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Open data
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Basic information
Entry | Database: PDB / ID: 8amp | |||||||||
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Title | Crystal structure of M.tuberculosis ferredoxin Fdx | |||||||||
![]() | Possible ferredoxin | |||||||||
![]() | ELECTRON TRANSPORT / Ferredoxin / tuberculosis / Rv0763c / CYP51 | |||||||||
Function / homology | FE3-S4 CLUSTER / : / Ferredoxin Fdx![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bukhdruker, S. / Kavaleuski, A. / Marin, E. / Kapranov, I. / Mishin, A. / Gilep, A. / Strushkevich, N. / Borshchevskiy, V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into 3Fe-4S ferredoxins diversity in M. tuberculosis highlighted by a first redox complex with P450. Authors: Gilep, A. / Varaksa, T. / Bukhdruker, S. / Kavaleuski, A. / Ryzhykau, Y. / Smolskaya, S. / Sushko, T. / Tsumoto, K. / Grabovec, I. / Kapranov, I. / Okhrimenko, I. / Marin, E. / Shevtsov, M. ...Authors: Gilep, A. / Varaksa, T. / Bukhdruker, S. / Kavaleuski, A. / Ryzhykau, Y. / Smolskaya, S. / Sushko, T. / Tsumoto, K. / Grabovec, I. / Kapranov, I. / Okhrimenko, I. / Marin, E. / Shevtsov, M. / Mishin, A. / Kovalev, K. / Kuklin, A. / Gordeliy, V. / Kaluzhskiy, L. / Gnedenko, O. / Yablokov, E. / Ivanov, A. / Borshchevskiy, V. / Strushkevich, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.1 KB | Display | ![]() |
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PDB format | ![]() | 26.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 852.6 KB | Display | ![]() |
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Full document | ![]() | 852.6 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 5.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8amoC ![]() 8amqC ![]() 1vjwS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 8519.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-F3S / |
#3: Chemical | ChemComp-FE / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 28, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→28.76 Å / Num. obs: 4958 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 38.46 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.097 / Net I/σ(I): 10.95 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VJW Resolution: 2→28.76 Å / SU ML: 0.2447 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.4958 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.76 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -10.2235812771 Å / Origin y: -10.5283877981 Å / Origin z: -13.6477102063 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 2 through 202) |