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- PDB-4xf9: cysteine dioxygenase variant - C93A at pH 8.0 in complex with hom... -

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Basic information

Entry
Database: PDB / ID: 4xf9
Titlecysteine dioxygenase variant - C93A at pH 8.0 in complex with homocysteine
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cupin Fold / cysteine to cysteine sulfinic acid catalysis / thiol dioxygenase
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
: / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsDriggers, C.M. / Karplus, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)NIH-DK-056649 United States
Department of Energy (DOE, United States)DE-AC02-98CH10886 United States
CitationJournal: J. Mol. Biol. / Year: 2016
Title: Structure-Based Insights into the Role of the Cys-Tyr Crosslink and Inhibitor Recognition by Mammalian Cysteine Dioxygenase.
Authors: Driggers, C.M. / Kean, K.M. / Hirschberger, L.L. / Cooley, R.B. / Stipanuk, M.H. / Karplus, P.A.
History
DepositionDec 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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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)23,2183
Polymers23,0271
Non-polymers1912
Water5,441302
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-I


Mass: 23026.822 Da / Num. of mol.: 1 / Mutation: C93A
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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M tri-sodium citrate pH=5.6, 24% PEG 4000, 0.15M ammonium acetate. 1:1 drop ratio with microseeding.; Soak solution at pH 8.0
PH range: 5.6-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2014
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.3→34 Å / Num. all: 43282 / Num. obs: 43245 / % possible obs: 84.2 % / Redundancy: 26.7 % / Net I/σ(I): 21.3
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 1.2 / % possible all: 36.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ieu

4ieu


Resolution: 1.3→33.907 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 4205 9.72 %same 5% as 4ieu
Rwork0.1566 ---
obs0.1595 43245 83.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→33.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 9 302 1816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011661
X-RAY DIFFRACTIONf_angle_d1.2652261
X-RAY DIFFRACTIONf_dihedral_angle_d13.88628
X-RAY DIFFRACTIONf_chiral_restr0.08241
X-RAY DIFFRACTIONf_plane_restr0.006298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.2836460.2999513X-RAY DIFFRACTION33
1.3148-1.33020.3218510.3007579X-RAY DIFFRACTION38
1.3302-1.34640.2925660.283654X-RAY DIFFRACTION43
1.3464-1.36350.2953820.2615681X-RAY DIFFRACTION45
1.3635-1.38140.2367680.2556767X-RAY DIFFRACTION50
1.3814-1.40040.3174860.245858X-RAY DIFFRACTION56
1.4004-1.42040.2593800.2418939X-RAY DIFFRACTION61
1.4204-1.44160.25251160.23391022X-RAY DIFFRACTION66
1.4416-1.46410.21661180.22721104X-RAY DIFFRACTION74
1.4641-1.48810.22921390.19571274X-RAY DIFFRACTION83
1.4881-1.51380.21821760.18651481X-RAY DIFFRACTION96
1.5138-1.54130.20061510.1741457X-RAY DIFFRACTION97
1.5413-1.57090.21131830.1811482X-RAY DIFFRACTION97
1.5709-1.6030.18541780.15881462X-RAY DIFFRACTION97
1.603-1.63780.15641440.1591510X-RAY DIFFRACTION97
1.6378-1.67590.18921710.15451478X-RAY DIFFRACTION97
1.6759-1.71790.20351720.16161492X-RAY DIFFRACTION98
1.7179-1.76430.16671580.171506X-RAY DIFFRACTION98
1.7643-1.81620.17661540.16261524X-RAY DIFFRACTION98
1.8162-1.87480.20031560.15021523X-RAY DIFFRACTION98
1.8748-1.94180.18671490.15281536X-RAY DIFFRACTION98
1.9418-2.01960.17751790.14631513X-RAY DIFFRACTION99
2.0196-2.11150.17641780.14751516X-RAY DIFFRACTION98
2.1115-2.22280.1681530.14381565X-RAY DIFFRACTION99
2.2228-2.3620.17721650.14281529X-RAY DIFFRACTION99
2.362-2.54430.17051610.15691584X-RAY DIFFRACTION99
2.5443-2.80030.20811830.15081552X-RAY DIFFRACTION99
2.8003-3.20520.18071810.15991586X-RAY DIFFRACTION99
3.2052-4.03710.19111740.14071609X-RAY DIFFRACTION99
4.0371-33.91840.15751870.14121744X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.2493 Å / Origin y: 3.0038 Å / Origin z: -49.79 Å
111213212223313233
T0.0723 Å20.0013 Å2-0.0042 Å2-0.0961 Å20.0016 Å2--0.0817 Å2
L1.1392 °20.4655 °2-0.2325 °2-1.1038 °20.2468 °2--0.9073 °2
S0.0152 Å °-0.0208 Å °0.0168 Å °0.0198 Å °-0.0072 Å °0.0109 Å °0.0505 Å °-0.0375 Å °0.0053 Å °
Refinement TLS groupSelection details: chain 'A' and resid 5 through 190

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