+Open data
-Basic information
Entry | Database: PDB / ID: 5fdb | ||||||
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Title | Iron free rat cysteine dioxygenase R60QC164R variant | ||||||
Components | Cysteine dioxygenase type 1 | ||||||
Keywords | OXIDOREDUCTASE / thioether bond / post-translational modification / post translational / posttranslational / cysteine dioxygenase / iron / non-heme mono-iron / cupin / arginine to glutamine substitution / cysteine to arginine substitution / beta barrel | ||||||
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 / Resolution: 1.75 Å | ||||||
Model details | R60QC164R variant | ||||||
Authors | Fellner, M. / Davies, C.G. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M. | ||||||
Citation | Journal: To be published Title: Iron free rat cysteine dioxygenase R60QC164R variant Authors: 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 | 5fdb.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fdb.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fdb ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fdb | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23083.875 Da / Num. of mol.: 1 / Mutation: R60Q,C164R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Plasmid: pPR-IBA1/RatCDO/R60QC164R_Variant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P21816, cysteine dioxygenase |
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#2: 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: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Hanging drops of 1 uL of 31.7 mg/mL R60QC164R CDO which had been iron reconstituted to 57% occupancy [100mM Tris-HCl, 50mM NaCl pH 8.0] and 2 uL of reservoir buffer containing crushed WT CDO ...Details: Hanging drops of 1 uL of 31.7 mg/mL R60QC164R CDO which had been iron reconstituted to 57% occupancy [100mM Tris-HCl, 50mM NaCl pH 8.0] and 2 uL of reservoir buffer containing crushed WT CDO seeds were allowed to equilibrate above the reservoir buffer [26% (w/v) polyethylene glycol 4000, 200 mM ammonium acetate, and 100 mM sodium citrate (pH 6.2)]. |
-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: Jun 26, 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: 1.75→57.19 Å / Num. obs: 21417 / % possible obs: 99.9 % / Redundancy: 11.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.03 / Net I/σ(I): 14.5 / Num. measured all: 244273 / Scaling rejects: 2831 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KWJ Resolution: 1.75→33.796 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.98 / 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: 80.95 Å2 / Biso mean: 22.5136 Å2 / Biso min: 4.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→33.796 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: 14
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