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- PDB-6dy8: Mn(II)-bound structure of the engineered cyt cb562 variant, CH2EY -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dy8 | |||||||||
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Title | Mn(II)-bound structure of the engineered cyt cb562 variant, CH2EY | |||||||||
![]() | Soluble cytochrome b562 | |||||||||
![]() | METAL BINDING PROTEIN / ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tezcan, F.A. / Rittle, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: An efficient, step-economical strategy for the design of functional metalloproteins. Authors: Rittle, J. / Field, M.J. / Green, M.T. / 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 | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 81.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6dy4C ![]() 6dy6C ![]() 6dybC ![]() 6dycC ![]() 6dydC ![]() 6dyeC ![]() 6dyfC ![]() 6dygC ![]() 6dyhC ![]() 6dyiC ![]() 6dyjC ![]() 6dykC ![]() 6dylC ![]() 2bc5S C: citing same article ( S: Starting model for refinement |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11913.368 Da / Num. of mol.: 4 / Mutation: K59W, I67H, G70Y, Q71H, T96C, T97E, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEC / ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.97 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Drop consists of 1 uL of 25% PEG 1500, 200 mM Calcium Chloride, and 0.1 M Tris (pH 8.5) mixed with 1 uL of 3.5 mM protein and 3.5 mM Manganese(II)Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→37.59 Å / Num. obs: 33090 / % possible obs: 98 % / Redundancy: 2.7 % / CC1/2: 0.978 / Rmerge(I) obs: 0.134 / Net I/σ(I): 3.2 |
Reflection shell | Resolution: 1.9→1.9514 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1 / Num. unique obs: 3296 / CC1/2: 0.832 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2bc5 Resolution: 1.9→37.59 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→37.59 Å
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Refine LS restraints |
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LS refinement shell |
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