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- PDB-5i0u: Incompletely interpreted D-cysteine soak of Cysteine Dioxygenase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i0u | ||||||
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Title | Incompletely interpreted D-cysteine soak of Cysteine Dioxygenase at pH 7.0 | ||||||
![]() | Cysteine dioxygenase type 1 | ||||||
![]() | OXIDOREDUCTASE / cupin-fold / cysteine to cysteine sulfinate / C93-Y157 crosslink / D-cysteine / catalysis oxidation | ||||||
Function / homology | ![]() L-cysteine metabolic 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 ...L-cysteine metabolic 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 / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kean, K.M. / Driggers, C.M. / Karplus, P.A. | ||||||
![]() | ![]() Title: Structure-Based Insights into the Role of the Cys-Tyr Crosslink and Inhibitor Recognition by Mammalian Cysteine Dioxygenase. Authors: Driggers, C.M. / Kean, K.M. / Hirschberger, L.L. / Cooley, R.B. / Stipanuk, M.H. / Karplus, P.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 | ![]() | 138.1 KB | Display | ![]() |
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PDB format | ![]() | 109.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.3 KB | Display | ![]() |
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Full document | ![]() | 438.4 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pixC ![]() 4piyC ![]() 4pizC ![]() 4pjyC ![]() 4xetC ![]() 4xezC ![]() 4xf0C ![]() 4xf1C ![]() 4xf3C ![]() 4xf4C ![]() 4xf9C ![]() 4xfbC ![]() 4xfcC ![]() 4xffC ![]() 4xfgC ![]() 4xfhC ![]() 4xfiC ![]() 5i0rC ![]() 5i0sC ![]() 5i0tC ![]() 4ieoS 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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Unit cell |
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Components
#1: Protein | Mass: 23090.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-DCY / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M tri-sodium citrate pH 5.6, 24% PEG 4000, 0.15 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→52.12 Å / Num. obs: 57647 / % possible obs: 100 % / Redundancy: 45.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 20.8 % / Mean I/σ(I) obs: 1.1 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4IEO Resolution: 1.25→52.118 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→52.118 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -17.07 Å / Origin y: 2.6998 Å / Origin z: -49.8024 Å
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Refinement TLS group | Selection details: chain 'A' and resid 5 through 190 |