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Open data
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Basic information
Entry | Database: PDB / ID: 6hlm | ||||||
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Title | Variant G129D of NuoEF from Aquifex aeolicus bound to NAD+ | ||||||
![]() | (NADH-quinone oxidoreductase subunit ...) x 2 | ||||||
![]() | ELECTRON TRANSPORT / Complex I / NuoEF / electron transfer / Aquifex aeolicus | ||||||
Function / homology | ![]() Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gerhardt, S. / Friedrich, T. / Einsle, O. / Gnandt, E. / Schulte, M. / Fiegen, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I. Authors: Schulte, M. / Frick, K. / Gnandt, E. / Jurkovic, S. / Burschel, S. / Labatzke, R. / Aierstock, K. / Fiegen, D. / Wohlwend, D. / Gerhardt, S. / Einsle, O. / Friedrich, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 483.2 KB | Display | ![]() |
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PDB format | ![]() | 394.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6hl2C ![]() 6hl3C ![]() 6hl4C ![]() 6hlaC ![]() 6hliC ![]() 6hljC ![]() 6q9cC ![]() 6q9gC ![]() 6q9jC ![]() 6q9kC ![]() 6r7pC 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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2 | ![]()
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Unit cell |
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Components
-NADH-quinone oxidoreductase subunit ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 18631.656 Da / Num. of mol.: 2 / Mutation: G129D Source method: isolated from a genetically manipulated source Details: G129D variant of NuoE / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 48523.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sequence contains C-terminal 6xHis Expression-tag / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 508 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NA / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.1M Tris/HCl 0.1M Sodium citrate / PH range: 6.9 - 7.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2013 / Details: OSMIC VARIMAX HF |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→88.55 Å / Num. obs: 114854 / % possible obs: 90.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 27.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.037 / Rsym value: 0.035 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5845 / CC1/2: 0.602 / Rpim(I) all: 0.509 / Rsym value: 0.508 / % possible all: 92.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: IN-HOUSE Resolution: 1.8→51.49 Å / Cor.coef. Fo:Fc: 0.9562 / Cor.coef. Fo:Fc free: 0.9477 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.107
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Displacement parameters | Biso mean: 34.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→51.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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