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Open data
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Basic information
Entry | Database: PDB / ID: 7yzm | ||||||
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Title | MgADPNP-bound DCCP:DCCP-R complex | ||||||
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![]() | OXIDOREDUCTASE / double cubane cluster / ATP / 4Fe4S cluster / electron transfer | ||||||
Function / homology | ![]() hydro-lyase activity / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeoung, J.-H. / Dobbek, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for coupled ATP-driven electron transfer in the double-cubane cluster protein. Authors: Jeoung, J.H. / Nicklisch, S. / Dobbek, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 901.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 126.3 KB | Display | |
Data in CIF | ![]() | 187.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yylC ![]() 7yzqC ![]() 6enoS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 8 molecules ABCDGHEF
#1: Protein | Mass: 47952.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: CHY_0487 / Production host: ![]() ![]() #2: Protein | Mass: 26347.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: CHY_0488 / Production host: ![]() ![]() |
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-Non-polymers , 10 types, 2798 molecules ![](data/chem/img/BJ8.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BU3.gif)
![](data/chem/img/TAM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BU3.gif)
![](data/chem/img/TAM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-BJ8 / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-NH4 / #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-BU3 / ( #8: Chemical | #9: Chemical | ChemComp-MG / #10: Chemical | ChemComp-ANP / #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, TrisHCl pH 8.0,PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→46.26 Å / Num. obs: 257334 / % possible obs: 97.71 % / Redundancy: 5.48 % / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.82→1.88 Å / Num. unique obs: 24967 / CC1/2: 0.712 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ENO.pdb Resolution: 1.82→26.72 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 19.73 / Stereochemistry target values: ML
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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 max: 128.85 Å2 / Biso mean: 26.793 Å2 / Biso min: 3.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.82→26.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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