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- PDB-6cdn: Crystal structure of cysteine-bound ferrous form of the crosslink... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cdn | ||||||||||||
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Title | Crystal structure of cysteine-bound ferrous form of the crosslinked Cl-Tyr157 human cysteine dioxygenase | ||||||||||||
![]() | Cysteine dioxygenase type 1 | ||||||||||||
![]() | OXIDOREDUCTASE / Cysteine / Cys-Tyr cofactor / iron / unnatural amino acid | ||||||||||||
Function / homology | ![]() sulfur amino acid biosynthetic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding / response to amino acid ...sulfur amino acid biosynthetic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding / response to amino acid / response to glucocorticoid / response to cAMP / lactation / ferrous iron binding / response to ethanol / inflammatory response / zinc ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Liu, A. / Li, J. / Shin, I. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase. Authors: Li, J. / Griffith, W.P. / Davis, I. / Shin, I. / Wang, J. / Li, F. / Wang, Y. / Wherritt, D.J. / Liu, 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 | ![]() | 59.3 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bgfC ![]() 6bgmC ![]() 6bpsC ![]() 6bptC ![]() 6bpuC ![]() 6bpvC ![]() 6bpwC ![]() 6bpxC ![]() 6cdhC ![]() 2ic1S 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22980.201 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 119 molecules ![](data/chem/img/CYS.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CYS / | ||||
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#3: Chemical | ChemComp-FE2 / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, 2 M ammonium sulfate, 2% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→50 Å / Num. obs: 21288 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.76 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.059 / Rrim(I) all: 0.147 / Χ2: 1.088 / Net I/σ(I): 7.8 / Num. measured all: 121064 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2IC1 Resolution: 2.055→42.987 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.83 Å2 / Biso mean: 37.4611 Å2 / Biso min: 20.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.055→42.987 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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