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- PDB-7tep: Crystal structure of a Cu-bound cytochrome cb562 variant in the p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tep | ||||||||||||
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Title | Crystal structure of a Cu-bound cytochrome cb562 variant in the presence of reductant | ||||||||||||
![]() | Soluble cytochrome b562 | ||||||||||||
![]() | METAL BINDING PROTEIN / ![]() | ||||||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kakkis, A. / Golub, E. | ||||||||||||
Funding support | European Union, 3items
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![]() | ![]() Title: Redox- and metal-directed structural diversification in designed metalloprotein assemblies. Authors: Kakkis, A. / Golub, E. / Choi, T.S. / Tezcan, F.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.3 KB | Display | ![]() |
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PDB format | ![]() | 140.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7rwuC ![]() 7rwvC ![]() 7rwwC ![]() 7rwxC ![]() 7rwyC ![]() 7su2C ![]() 2bc5S 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: 11657.113 Da / Num. of mol.: 4 Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, D74A, K77H, T96C, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEC / ![]() #3: Chemical | ChemComp-CU / ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.39 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG1500, 0.1 M Bis-Tris, 0.2 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→48.3 Å / Num. obs: 9592 / % possible obs: 95.88 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05709 / Rpim(I) all: 0.03648 / Rrim(I) all: 0.06803 / Net I/σ(I): 16.66 |
Reflection shell | Resolution: 2.7→2.797 Å / Rmerge(I) obs: 0.1458 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 900 / CC1/2: 0.953 / Rpim(I) all: 0.0941 / Rrim(I) all: 0.1742 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2bc5 Resolution: 2.7→48.3 Å / SU ML: 0.5303 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.6677 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 28.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.3 Å
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Refine LS restraints |
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LS refinement shell |
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