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Open data
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Basic information
Entry | Database: PDB / ID: 4yni | ||||||
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Title | Iron free succinate bound rat cysteine dioxygenase | ||||||
![]() | Cysteine dioxygenase type 1![]() | ||||||
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Function / homology | ![]() L-cysteine metabolic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M. | ||||||
![]() | ![]() Title: Iron free succinate bound rat cysteine dioxygenase Authors: Fellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / 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 | ![]() | 56.2 KB | Display | ![]() |
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PDB format | ![]() | 38.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: 24259.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-SIN / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: Hanging drops of 1 microL of 15 mg/mL WT-CDO (10mM sodiumphosphate, 20mM NaCl pH 7.5) and 3 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (25% (w/v) ...Details: Hanging drops of 1 microL of 15 mg/mL WT-CDO (10mM sodiumphosphate, 20mM NaCl pH 7.5) and 3 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (25% (w/v) polyethylene glycol 1500, 13 mM succinate, 44 mM mono sodium phosphate, 44 mM glycine) and 0.6 microL WT-CDO seeds (grown in the reservoir buffer) |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 2, 2013 / Details: Osmic VariMax optics | |||||||||||||||||||||||||||
Radiation | Monochromator: Osmic VariMax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 2.4→41.89 Å / Num. obs: 15515 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 36.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.044 / Net I/σ(I): 11.5 / Num. measured all: 85493 / Scaling rejects: 168 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4KWJ Resolution: 2.404→41.89 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 23.67 / 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: 99.03 Å2 / Biso mean: 39.297 Å2 / Biso min: 20.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.404→41.89 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: 6
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