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- PDB-4iev: Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys -

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Basic information

Entry
Database: PDB / ID: 4iev
TitleCys-only bound Cysteine Dioxygenase at pH 8.0 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 / response to azide / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding ...L-cysteine metabolic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / response to azide / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding / response to cAMP / response to amino acid / lactation / response to glucocorticoid / 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 / : / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine dioxygenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2363
Polymers23,0591
Non-polymers1772
Water3,351186
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-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 / 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: 8.2.1 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2012
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→42 Å / Num. obs: 28421 / % possible obs: 100 % / 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: 1.6→33.91 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 2720 9.82 %
Rwork0.18 --
obs0.183 27708 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→33.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 8 186 1706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131575
X-RAY DIFFRACTIONf_angle_d1.3342137
X-RAY DIFFRACTIONf_dihedral_angle_d14.651582
X-RAY DIFFRACTIONf_chiral_restr0.087228
X-RAY DIFFRACTIONf_plane_restr0.006276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62910.35391060.38111065X-RAY DIFFRACTION82
1.6291-1.66040.38381520.36391251X-RAY DIFFRACTION99
1.6604-1.69430.3671510.35131314X-RAY DIFFRACTION100
1.6943-1.73120.3431560.33281266X-RAY DIFFRACTION100
1.7312-1.77140.36651250.31151324X-RAY DIFFRACTION100
1.7714-1.81570.31581340.28361315X-RAY DIFFRACTION100
1.8157-1.86480.30041300.25551308X-RAY DIFFRACTION100
1.8648-1.91970.28821350.2511321X-RAY DIFFRACTION100
1.9197-1.98160.27691450.23271324X-RAY DIFFRACTION100
1.9816-2.05250.2651550.19821291X-RAY DIFFRACTION100
2.0525-2.13460.23871490.19681322X-RAY DIFFRACTION100
2.1346-2.23180.25141330.16891321X-RAY DIFFRACTION100
2.2318-2.34940.23871390.17011321X-RAY DIFFRACTION100
2.3494-2.49650.23461380.16841345X-RAY DIFFRACTION100
2.4965-2.68920.26071690.18321310X-RAY DIFFRACTION100
2.6892-2.95970.23861410.1771349X-RAY DIFFRACTION100
2.9597-3.38760.18461540.16411374X-RAY DIFFRACTION100
3.3876-4.26680.1611430.13991377X-RAY DIFFRACTION100
4.2668-33.91450.171650.14781490X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.2383 Å / Origin y: 3.0621 Å / Origin z: -49.7928 Å
111213212223313233
T0.1134 Å2-0.004 Å2-0.0156 Å2-0.1888 Å2-0.018 Å2--0.135 Å2
L2.9421 °20.5804 °2-0.2713 °2-2.7962 °20.1685 °2--2.2293 °2
S-0.041 Å °-0.0118 Å °0.0805 Å °-0.0142 Å °0.0239 Å °0.0452 Å °0.1261 Å °-0.1352 Å °0.007 Å °
Refinement TLS groupSelection details: (CHAIN A AND (RESID 5:190 OR RESID 501:502 ) )

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