+Open data
-Basic information
Entry | Database: PDB / ID: 7yzq | ||||||
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Title | MgADP-AlF4-bound DCCP:DCCP-R complex | ||||||
Components |
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Keywords | OXIDOREDUCTASE / double cubane cluster / ATP / 4Fe4S cluster / electron transfer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Carboxydothermus hydrogenoformans Z-2901 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Jeoung, J.-H. / Dobbek, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yzq.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7yzq.ent.gz | 887.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/7yzq ftp://data.pdbj.org/pub/pdb/validation_reports/yz/7yzq | HTTPS FTP |
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-Related structure data
Related structure data | 7yylC 7yzmC 6enoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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 CDABEFGH
#1: Protein | Mass: 47952.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: CHY_0487 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3AET9 #2: Protein | Mass: 26347.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: CHY_0488 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3AET8 |
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-Non-polymers , 12 types, 2967 molecules
#3: Chemical | ChemComp-BJ8 / #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-TAM / #7: Chemical | ChemComp-BU3 / ( #8: Chemical | ChemComp-ADP / #9: Chemical | ChemComp-MG / #10: Chemical | ChemComp-ALF / #11: Chemical | #12: Chemical | ChemComp-SO4 / #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, Tris-HCl pH 8.0, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 28, 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: 1.96→46.16 Å / Num. obs: 202797 / % possible obs: 96.12 % / Redundancy: 3.51 % / CC1/2: 0.993 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.96→2.03 Å / Num. unique obs: 19327 / CC1/2: 0.697 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6eno Resolution: 1.96→46.16 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 23.39 / 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: 149.93 Å2 / Biso mean: 29.8558 Å2 / Biso min: 7.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.96→46.16 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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