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Yorodumi- PDB-3eln: A Putative Fe2+-bound Persulfenate Intermediate in Cysteine Dioxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eln | ||||||
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Title | A Putative Fe2+-bound Persulfenate Intermediate in Cysteine Dioxygenase | ||||||
Components | Cysteine dioxygenase type 1 | ||||||
Keywords | OXIDOREDUCTASE / Peroxysulfenate / Non-heme dioxygenases / Fe2+ metalloenzyme / cysteine / taurine / thioether / Dioxygenase / Iron / Metal-binding / Phosphoprotein / Thioether bond | ||||||
Function / homology | Function and homology information 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 / response to organonitrogen compound / lactation / ferrous iron binding / response to ethanol / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.42 Å | ||||||
Authors | Simmons, C.R. / Stipanuk, M.H. / Karplus, P.A. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: A putative Fe2+-bound persulfenate intermediate in cysteine dioxygenase. Authors: Simmons, C.R. / Krishnamoorthy, K. / Granett, S.L. / Schuller, D.J. / Dominy, J.E. / Begley, T.P. / Stipanuk, M.H. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eln.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eln.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 3eln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/3eln ftp://data.pdbj.org/pub/pdb/validation_reports/el/3eln | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23058.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21816, cysteine dioxygenase |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-2CO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Purified enzyme was concentrated to ~8 mg/mL and then added into a crystallization screen containing 0.1 M tri-sodium citrate pH=5.6, 24-34% PEG 4K, and 0.1-0.25 M ammonium acetate. 1.5L of ...Details: Purified enzyme was concentrated to ~8 mg/mL and then added into a crystallization screen containing 0.1 M tri-sodium citrate pH=5.6, 24-34% PEG 4K, and 0.1-0.25 M ammonium acetate. 1.5L of protein solution was added to each well and mixed with an equivalent volume of reservoir solution., VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→20 Å / Num. obs: 39648 / % possible obs: 100 % |
Reflection shell | Resolution: 1.42→1.45 Å / % possible all: 99.97 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.42→19.68 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.724 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.187 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→19.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.457 Å / Total num. of bins used: 20
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