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Open data
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Basic information
Entry | Database: PDB / ID: 4xfi | |||||||||
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Title | cysteine dioxygenase variant - Y157F at pH 6.2 with homocysteine | |||||||||
![]() | Cysteine dioxygenase type 1 | |||||||||
![]() | OXIDOREDUCTASE / Cupin Fold / cysteine to cysteine sulfinic acid catalysis / thiol dioxygenase | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Driggers, C.M. / Karplus, P.A. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 102.3 KB | Display | ![]() |
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PDB format | ![]() | 77.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.1 KB | Display | ![]() |
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Full document | ![]() | 437.2 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 18.7 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 ![]() 5i0rC ![]() 5i0sC ![]() 5i0tC ![]() 5i0uC ![]() 4ieuS 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
#1: Protein | Mass: 23042.889 Da / Num. of mol.: 1 / Mutation: Y157F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-HCS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1M tri-sodium citrate pH=5.6, 24% PEG 4000, 0.15M ammonium acetate. 1:1 drop ratio with microseeding.; Soak solution at pH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→33 Å / Num. all: 39877 / Num. obs: 39392 / % possible obs: 94.7 % / Redundancy: 23.3 % / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.1 / % possible all: 67.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ieu Resolution: 1.4→33 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.82 / 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: 1.4→33 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: -17.4493 Å / Origin y: 2.9762 Å / Origin z: -50.0681 Å
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Refinement TLS group | Selection details: chain 'A' and resid 5 through 190 |