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- PDB-6ldg: 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: 6ldg | ||||||
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Title | Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96I AB5 | ||||||
![]() | engineered cyt cb 562 variant, C96I AB | ||||||
![]() | 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 | ![]() | 66.3 KB | Display | ![]() |
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PDB format | ![]() | 46.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ldeC ![]() 6ldfC ![]() 7dclC ![]() 3iq6S 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
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 11832.235 Da / Num. of mol.: 2 / Fragment: variant, C96I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 207 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350, 100 mM HEPES pH 7.5, 200 mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→28.38 Å / Num. obs: 15931 / % possible obs: 99.8 % / Redundancy: 40 % / Rsym value: 0.129 / Net I/σ(I): 105.8 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 40.2 % / Num. unique obs: 760 / Rsym value: 0.323 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3IQ6 Resolution: 1.98→28.38 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.352 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.164 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.06 Å2 / Biso mean: 22.766 Å2 / Biso min: 7.91 Å2
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Refinement step | Cycle: final / Resolution: 1.98→28.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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