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- PDB-4ies: Cys-persulfenate bound Cysteine Dioxygenase at pH 6.2 in the pres... -

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Basic information

Entry
Database: PDB / ID: 4ies
TitleCys-persulfenate bound Cysteine Dioxygenase at pH 6.2 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 / response to organonitrogen compound / 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: 1.4 Å
AuthorsDriggers, C.M. / Cooley, R.B. / Sankaran, 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
Water4,324240
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
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

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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-FE / FE (III) ION / Iron


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 / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 1.4→29 Å / Num. obs: 41131 / % possible obs: 99.1 % / 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: 1.4→28.034 Å / SU ML: 0.19 / σ(F): 1.33 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.185 4005 9.81 %
Rwork0.1447 --
obs0.1487 40816 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→28.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 10 240 1758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121621
X-RAY DIFFRACTIONf_angle_d1.232197
X-RAY DIFFRACTIONf_dihedral_angle_d12.574602
X-RAY DIFFRACTIONf_chiral_restr0.078234
X-RAY DIFFRACTIONf_plane_restr0.006287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41650.40491040.36271001X-RAY DIFFRACTION80
1.4165-1.43380.34391180.35541130X-RAY DIFFRACTION88
1.4338-1.45190.36581160.3141172X-RAY DIFFRACTION94
1.4519-1.4710.36821450.30211231X-RAY DIFFRACTION97
1.471-1.49120.36781250.27921240X-RAY DIFFRACTION99
1.4912-1.51250.30921420.26421263X-RAY DIFFRACTION99
1.5125-1.5350.27741390.22751276X-RAY DIFFRACTION100
1.535-1.5590.24941280.2031261X-RAY DIFFRACTION100
1.559-1.58460.2521500.17271249X-RAY DIFFRACTION100
1.5846-1.61190.21291550.15841264X-RAY DIFFRACTION100
1.6119-1.64120.22081260.13491288X-RAY DIFFRACTION100
1.6412-1.67280.19271470.14271257X-RAY DIFFRACTION100
1.6728-1.70690.20551450.12951261X-RAY DIFFRACTION100
1.7069-1.7440.18711440.12311277X-RAY DIFFRACTION100
1.744-1.78460.17421370.12211272X-RAY DIFFRACTION100
1.7846-1.82920.21961320.11561282X-RAY DIFFRACTION100
1.8292-1.87870.16991210.10941282X-RAY DIFFRACTION100
1.8787-1.93390.19231330.10661319X-RAY DIFFRACTION100
1.9339-1.99630.16271510.10911268X-RAY DIFFRACTION100
1.9963-2.06770.17071550.10791262X-RAY DIFFRACTION100
2.0677-2.15040.13561350.10981302X-RAY DIFFRACTION100
2.1504-2.24820.17161300.10911294X-RAY DIFFRACTION100
2.2482-2.36670.18021400.12181296X-RAY DIFFRACTION100
2.3667-2.51490.20621290.13551317X-RAY DIFFRACTION100
2.5149-2.70890.18651670.14341288X-RAY DIFFRACTION100
2.7089-2.98130.1811360.1441314X-RAY DIFFRACTION100
2.9813-3.4120.15061500.14481342X-RAY DIFFRACTION100
3.412-4.29630.15991410.1351358X-RAY DIFFRACTION100
4.2963-28.040.17421640.16421445X-RAY DIFFRACTION100

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