+Open data
-Basic information
Entry | Database: PDB / ID: 4ysf | ||||||
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Title | Resting state of rat cysteine dioxygenase H155N variant | ||||||
Components | Cysteine dioxygenase type 1 | ||||||
Keywords | OXIDOREDUCTASE / cupin / crosslink | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | ||||||
Model details | H155N variant | ||||||
Authors | Fellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M. | ||||||
Citation | Journal: To be published Title: Resting state of rat cysteine dioxygenase H155N variant Authors: Fellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ysf.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ysf.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ysf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/4ysf ftp://data.pdbj.org/pub/pdb/validation_reports/ys/4ysf | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24235.150 Da / Num. of mol.: 1 / Mutation: H155N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Plasmid: pPR-IBA1/RatCDO/H155N_Variant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P21816, cysteine dioxygenase |
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#2: Chemical | ChemComp-FE2 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.43 % |
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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 24 mg/mL H155N-CDO (10 mM sodiumphosphate, 20 mM NaCl pH 7.5) and 2.5 microL reservoir buffer containg H155N-CDO crushed seeds were allowed to ...Details: Hanging drops of 2.5 microL of approximately 24 mg/mL H155N-CDO (10 mM sodiumphosphate, 20 mM NaCl pH 7.5) and 2.5 microL reservoir buffer containg H155N-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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 3, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.94→41.75 Å / Num. obs: 15885 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 22.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.028 / Net I/σ(I): 26.2 / Num. measured all: 222857 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KWJ Resolution: 1.94→33.745 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.87 / 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: 90.36 Å2 / Biso mean: 26.7991 Å2 / Biso min: 9.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→33.745 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: 10 / % reflection obs: 100 %
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