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- PDB-6ldf: Crystal structure of the Zn-directed tetramer of the engineered c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ldf | ||||||
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Title | Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96K AB5 | ||||||
![]() | engineered cyt cb 562 variant, C96K AB5 | ||||||
![]() | ELECTRON TRANSPORT / Artificial enzyme / Metallohydrolase / Directed evolution / METAL BINDING PROTEIN | ||||||
Function / homology | HEME C![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Song, W.J. / Yu, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes. Authors: Yu, J. / Yang, J. / Seok, C. / Song, W.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64 KB | Display | ![]() |
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PDB format | ![]() | 45.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.1 MB | Display | ![]() |
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Full document | ![]() | 4.1 MB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ldeC ![]() 6ldgC ![]() 7dclC ![]() 3qi5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11848.258 Da / Num. of mol.: 2 / Mutation: variant, C96K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #5: 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: 2.23 Å3/Da / Density % sol: 44.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 45% (+/-)-2-methyl-2,4-pentanediol (MPD), 100 mM bis-tris, 200 mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→28.62 Å / Num. obs: 9893 / % possible obs: 99.7 % / Redundancy: 39.4 % / Rsym value: 0.108 / Net I/σ(I): 95.02 |
Reflection shell | Resolution: 2.35→2.39 Å / Num. unique obs: 470 / Rsym value: 0.433 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QI5 Resolution: 2.35→28.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.12 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.412 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.45 Å2 / Biso mean: 48.278 Å2 / Biso min: 18.71 Å2
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Refinement step | Cycle: final / Resolution: 2.35→28.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.354→2.415 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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