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- PDB-6dyl: Vanadyl-bound structure of the engineered cyt b562 variant, CH3Y* -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dyl | |||||||||
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Title | Vanadyl-bound structure of the engineered cyt b562 variant, CH3Y* | |||||||||
![]() | Soluble cytochrome b562 | |||||||||
![]() | METAL BINDING PROTEIN / Designed protein / 4-helix bundle | |||||||||
Function / homology | ![]() electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding 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 | ![]() | 169.7 KB | Display | ![]() |
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PDB format | ![]() | 135.2 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 ![]() 6dy8C ![]() 6dybC ![]() 6dycC ![]() 6dydC ![]() 6dyeC ![]() 6dyfC ![]() 6dygC ![]() 6dyhC ![]() 6dyiC ![]() 6dyjC ![]() 6dykC ![]() 1m6tS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 11930.375 Da / Num. of mol.: 4 Mutation: M7W, K59W, I67H, G70Y, Q71H, T96C, T97H, Y101A, H102I, R106L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Drop consists of 1 uL of 35% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 5.5) mixed with 1 uL of 4 mM protein and 2.2 mM Vanadyl Sulfate (Anaerobic crystal growth) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.691→49.2 Å / Num. obs: 48286 / % possible obs: 98.59 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.02 |
Reflection shell | Resolution: 1.691→1.7587 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.3342 / Mean I/σ(I) obs: 7.92 / Num. unique obs: 4705 / CC1/2: 0.972 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1m6t Resolution: 1.691→49.2 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.691→49.2 Å
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Refine LS restraints |
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LS refinement shell |
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