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- PDB-8bj8: Desulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Htra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bj8 | ||||||
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Title | Desulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Htrans-like state | ||||||
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![]() | OXIDOREDUCTASE / [FeFe] Hydrogenase / C178A mutant | ||||||
Function / homology | ![]() ferredoxin hydrogenase / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bikbaev, K. / Span, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Binding of exogenous cyanide reveals new active-site states in [FeFe] hydrogenases. Authors: Martini, M.A. / Bikbaev, K. / Pang, Y. / Lorent, C. / Wiemann, C. / Breuer, N. / Zebger, I. / DeBeer, S. / Span, I. / Bjornsson, R. / Birrell, J.A. / Rodriguez-Macia, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.6 KB | Display | ![]() |
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PDB format | ![]() | 155.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bj7C ![]() 6sg2S 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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Unit cell |
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Components
#1: Protein | Mass: 43191.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 10082.425 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-VHR / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.88 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1.01→44.602 Å / Num. obs: 200463 / % possible obs: 99.3 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.01→1.03 Å / Redundancy: 8.7 % / Rmerge(I) obs: 2.148 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 9215 / CC1/2: 0.338 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6SG2 Resolution: 1.01→44.602 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.153 / WRfactor Rwork: 0.14 / SU B: 0.366 / SU ML: 0.018 / Average fsc free: 0.9765 / Average fsc work: 0.9781 / Cross valid method: FREE R-VALUE / ESU R: 0.024 / ESU R Free: 0.025 Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.456 Å2
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Refinement step | Cycle: LAST / Resolution: 1.01→44.602 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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