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- PDB-4jtn: Cysteine Dioxygenase at pH 8.0 in the presence of dithionite -

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Basic information

Entry
Database: PDB / ID: 4jtn
TitleCysteine Dioxygenase at pH 8.0 in the presence of dithionite
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cupin fold / cysteine to cysteine sulfinic acid catalysis / 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 dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.593 Å
AuthorsDriggers, C.M. / 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
DepositionMar 23, 2013Deposition 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 16, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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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
Water4,270237
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.: 237 / 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: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M tri-sodium citrate pH=5.6, 24% PEG 4000, 0.15M ammonium acetate. 1:1 drop ratio with microseeding., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2013
RadiationMonochromator: Si 111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.593→29 Å / Num. all: 25267 / Num. obs: 25267 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.593→28.8 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 2465 9.78 %Same test set 4IEU
Rwork0.1708 ---
obs0.1735 25199 88.88 %-
all-25267 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.593→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 1 237 1734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161588
X-RAY DIFFRACTIONf_angle_d1.3762164
X-RAY DIFFRACTIONf_dihedral_angle_d14.005582
X-RAY DIFFRACTIONf_chiral_restr0.091229
X-RAY DIFFRACTIONf_plane_restr0.007284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5935-1.62410.24121270.23781130X-RAY DIFFRACTION83
1.6241-1.65720.27521550.22451337X-RAY DIFFRACTION96
1.6572-1.69330.24151570.21091373X-RAY DIFFRACTION99
1.6933-1.73270.23051170.20161040X-RAY DIFFRACTION75
1.7327-1.7760.21231470.18281396X-RAY DIFFRACTION100
1.776-1.8240.22321380.17021403X-RAY DIFFRACTION100
1.824-1.87770.23471370.17011405X-RAY DIFFRACTION100
1.8777-1.93820.2469870.198866X-RAY DIFFRACTION63
1.9382-2.00750.22811330.16091026X-RAY DIFFRACTION94
2.0075-2.08790.19831330.16971057X-RAY DIFFRACTION76
2.0879-2.18290.22041420.16281423X-RAY DIFFRACTION100
2.1829-2.29790.20751020.16591067X-RAY DIFFRACTION75
2.2979-2.44180.19111450.16741428X-RAY DIFFRACTION100
2.4418-2.63020.22571620.16791430X-RAY DIFFRACTION100
2.6302-2.89470.20671310.17431191X-RAY DIFFRACTION83
2.8947-3.3130.18341610.17051441X-RAY DIFFRACTION100
3.313-4.1720.16661230.15941141X-RAY DIFFRACTION77
4.172-28.80470.17011680.161580X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.0531 Å / Origin y: 3.4112 Å / Origin z: -49.517 Å
111213212223313233
T0.1281 Å20.003 Å2-0.0061 Å2-0.1677 Å20.0103 Å2--0.1503 Å2
L1.3059 °20.5977 °2-0.1808 °2-1.8002 °20.2294 °2--1.2239 °2
S0.0118 Å °-0.0395 Å °-0.0579 Å °0.0342 Å °-0.0232 Å °-0.015 Å °0.079 Å °-0.0409 Å °0.0125 Å °
Refinement TLS groupSelection details: all

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