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- PDB-4ier: Cys-persulfenate bound Cysteine Dioxygenase at pH 5.5 in the pres... -

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Basic information

Entry
Database: PDB / ID: 4ier
TitleCys-persulfenate bound Cysteine Dioxygenase at pH 5.5 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
S-HYDROPEROXYCYSTEINE / : / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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)23,2683
Polymers23,0591
Non-polymers2092
Water3,783210
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: Chemical ChemComp-2CO / S-HYDROPEROXYCYSTEINE


Type: L-peptide linking / Mass: 153.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 5.0.1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2010
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.45→42 Å / Num. obs: 33402 / % possible obs: 88.3 % / 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: 1.45→40.729 Å / SU ML: 0.17 / σ(F): 1.33 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 3225 9.83 %
Rwork0.1366 --
obs0.1426 32808 87.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→40.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 10 210 1732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131599
X-RAY DIFFRACTIONf_angle_d1.2522161
X-RAY DIFFRACTIONf_dihedral_angle_d12.883588
X-RAY DIFFRACTIONf_chiral_restr0.078230
X-RAY DIFFRACTIONf_plane_restr0.005282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4501-1.47170.4054610.3257498X-RAY DIFFRACTION35
1.4717-1.49470.332730.3048732X-RAY DIFFRACTION51
1.4947-1.51920.3662900.2895817X-RAY DIFFRACTION56
1.5192-1.54540.3456920.256923X-RAY DIFFRACTION64
1.5454-1.57350.30011280.2379968X-RAY DIFFRACTION68
1.5735-1.60380.30351250.22541056X-RAY DIFFRACTION74
1.6038-1.63650.28651110.19231165X-RAY DIFFRACTION80
1.6365-1.67210.27051430.17081275X-RAY DIFFRACTION89
1.6721-1.7110.23711640.15631379X-RAY DIFFRACTION96
1.711-1.75380.21191470.14021446X-RAY DIFFRACTION99
1.7538-1.80120.2511580.12641449X-RAY DIFFRACTION100
1.8012-1.85420.20021390.11811479X-RAY DIFFRACTION100
1.8542-1.91410.20161490.11211443X-RAY DIFFRACTION100
1.9141-1.98250.18461600.11471468X-RAY DIFFRACTION100
1.9825-2.06190.19551790.10691427X-RAY DIFFRACTION100
2.0619-2.15570.17181590.10391464X-RAY DIFFRACTION100
2.1557-2.26930.21530.1041474X-RAY DIFFRACTION100
2.2693-2.41150.19211350.11911509X-RAY DIFFRACTION100
2.4115-2.59770.20821720.12711459X-RAY DIFFRACTION100
2.5977-2.8590.2071750.13441477X-RAY DIFFRACTION100
2.859-3.27260.20491690.14381499X-RAY DIFFRACTION100
3.2726-4.12250.16821640.1311545X-RAY DIFFRACTION100
4.1225-40.74540.18061790.15291631X-RAY DIFFRACTION100

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