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- PDB-4ieq: unliganded Cysteine Dioxygenase at pH 5.0 in the presence of Cys -

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Basic information

Entry
Database: PDB / ID: 4ieq
Titleunliganded Cysteine Dioxygenase at pH 5.0 in the presence of Cys
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cupin fold / catalyzes oxidation / cysteine to cysteine sulfinate / C93-Y157 crosslink / Cytosol
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 / lactation / ferrous iron binding / response to ethanol / zinc ion binding / cytosol
Similarity search - Function
Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.396 Å
AuthorsDriggers, C.M. / Cooley, R.B. / Karplus, P.A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Cysteine Dioxygenase Structures from pH4 to 9: Consistent Cys-Persulfenate Formation at Intermediate pH and a Cys-Bound Enzyme at Higher pH.
Authors: Driggers, C.M. / Cooley, R.B. / Sankaran, B. / Hirschberger, L.L. / Stipanuk, M.H. / Karplus, P.A.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine dioxygenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1152
Polymers23,0591
Non-polymers561
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.600, 57.600, 122.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cysteine dioxygenase type 1 / Cysteine dioxygenase type I / CDO / CDO-I


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) / References: UniProt: P21816, cysteine dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
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., pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2012
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.396→34 Å / Num. obs: 34382 / % possible obs: 82.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.396→33.907 Å / SU ML: 0.14 / σ(F): 1.33 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 3319 9.77 %
Rwork0.1431 --
obs0.148 33978 81.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.396→33.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 1 216 1729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111678
X-RAY DIFFRACTIONf_angle_d1.2622281
X-RAY DIFFRACTIONf_dihedral_angle_d13.804645
X-RAY DIFFRACTIONf_chiral_restr0.082244
X-RAY DIFFRACTIONf_plane_restr0.006298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3955-1.41550.4094750.309807X-RAY DIFFRACTION52
1.4155-1.43660.3039990.2787945X-RAY DIFFRACTION61
1.4366-1.4590.3189700.2411612X-RAY DIFFRACTION40
1.459-1.4830.2615660.2358648X-RAY DIFFRACTION42
1.483-1.50850.26631270.20221183X-RAY DIFFRACTION77
1.5085-1.5360.301820.1806838X-RAY DIFFRACTION54
1.536-1.56550.2591570.1391391X-RAY DIFFRACTION91
1.5655-1.59750.19291730.12671510X-RAY DIFFRACTION98
1.5975-1.63220.19411710.11721539X-RAY DIFFRACTION99
1.6322-1.67020.18761780.10651523X-RAY DIFFRACTION100
1.6702-1.71190.17291830.10931535X-RAY DIFFRACTION100
1.7119-1.75820.1771240.1141239X-RAY DIFFRACTION78
1.7582-1.80990.2031570.11711568X-RAY DIFFRACTION100
1.8099-1.86840.19111610.12181563X-RAY DIFFRACTION100
1.8684-1.93510.2244990.14851039X-RAY DIFFRACTION66
1.9351-2.01260.17631440.11731115X-RAY DIFFRACTION73
2.0126-2.10420.17791480.11881216X-RAY DIFFRACTION79
2.1042-2.21510.18971460.12241601X-RAY DIFFRACTION99
2.2151-2.35380.21551280.12891158X-RAY DIFFRACTION74
2.3538-2.53550.20461620.13891609X-RAY DIFFRACTION100
2.5355-2.79060.23161570.14231356X-RAY DIFFRACTION85
2.7906-3.19410.19341770.14951615X-RAY DIFFRACTION100
3.1941-4.02320.18331450.14421308X-RAY DIFFRACTION80
4.0232-33.91690.1641900.16381741X-RAY DIFFRACTION99

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