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Open data
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Basic information
Entry | Database: PDB / ID: 5efu | ||||||
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Title | Resting state of rat cysteine dioxygenase H155Q variant | ||||||
![]() | Cysteine dioxygenase type 1 | ||||||
![]() | OXIDOREDUCTASE / cysteine dioxygenase / non-heme mono-iron / Cupin / histidine to glutamine substitution | ||||||
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 | ![]() ![]() ![]() | ||||||
Model details | H155Q variant | ||||||
![]() | Fellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M. | ||||||
![]() | ![]() Title: Resting state of rat cysteine dioxygenase H155Q variant Authors: Fellner, M. / Wilbanks, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54 KB | Display | ![]() |
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PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.4 KB | Display | ![]() |
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Full document | ![]() | 430.5 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kwjS 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: 24249.178 Da / Num. of mol.: 1 / Mutation: H155Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FE2 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Hanging drops of 2.5 microL of approximately 25 mg/mL H155Q-CDO (10 mM sodiumphosphate, 20 mM NaCl pH 7.5) and 2.5 microL reservoir buffer containg H155Q-CDO crushed seeds were allowed to ...Details: Hanging drops of 2.5 microL of approximately 25 mg/mL H155Q-CDO (10 mM sodiumphosphate, 20 mM NaCl pH 7.5) and 2.5 microL reservoir buffer containg H155Q-CDO crushed seeds were allowed to equilibrate above the reservoir buffer (26% (w/v) polyethylene glycol 4000, 200 mM ammonium acetate, 100 mM sodium citrate). |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.8→57.61 Å / Num. obs: 5403 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 47 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Net I/σ(I): 14.1 / Num. measured all: 35296 / Scaling rejects: 238 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KWJ Resolution: 2.8→28.805 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.26 / 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 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 120.97 Å2 / Biso mean: 45.7557 Å2 / Biso min: 14.56 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→28.805 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %
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