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- PDB-4xfa: cysteine dioxygenase variant - Y157F at pH 8.0 in complex with ho... -

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Basic information

Entry
Database: PDB / ID: 4xfa
Titlecysteine dioxygenase variant - Y157F 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 / 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
: / 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: 1.65 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: To Be Published
Title: Structures of Mammalian Cysteine Dioxygenase Variants Missing the Cys-Tyr Crosslink
Authors: Driggers, C.M. / Hischberger, L.L. / 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 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Apr 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)23,2343
Polymers23,0431
Non-polymers1912
Water3,279182
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: 23042.889 Da / Num. of mol.: 1 / Mutation: Y157F
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.: 182 / 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: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
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
Temp details: 290-298

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2013
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→33 Å / Num. all: 25597 / Num. obs: 25071 / % possible obs: 98.9 % / Redundancy: 27.4 % / Net I/σ(I): 26.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 22.8 % / Mean I/σ(I) obs: 2 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ieu

4ieu


Resolution: 1.65→33 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 2448 9.76 %same 5% as 4ieu
Rwork0.1691 ---
obs0.1731 25071 97.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 9 182 1698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131617
X-RAY DIFFRACTIONf_angle_d1.332196
X-RAY DIFFRACTIONf_dihedral_angle_d13.61605
X-RAY DIFFRACTIONf_chiral_restr0.056236
X-RAY DIFFRACTIONf_plane_restr0.007289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.68370.30251280.24381123X-RAY DIFFRACTION87
1.6837-1.72030.28731490.24611291X-RAY DIFFRACTION97
1.7203-1.76030.22771390.22861307X-RAY DIFFRACTION98
1.7603-1.80440.28291310.23431317X-RAY DIFFRACTION98
1.8044-1.85310.28511310.21071325X-RAY DIFFRACTION98
1.8531-1.90770.24661340.20811308X-RAY DIFFRACTION98
1.9077-1.96920.2041320.20421308X-RAY DIFFRACTION98
1.9692-2.03960.26431540.19121313X-RAY DIFFRACTION98
2.0396-2.12130.19921580.18531307X-RAY DIFFRACTION99
2.1213-2.21780.23461320.17731350X-RAY DIFFRACTION99
2.2178-2.33470.22841460.17591337X-RAY DIFFRACTION99
2.3347-2.48090.25451350.18181336X-RAY DIFFRACTION99
2.4809-2.67240.2271560.18411341X-RAY DIFFRACTION99
2.6724-2.94120.22761550.17681364X-RAY DIFFRACTION99
2.9412-3.36640.20021550.17031373X-RAY DIFFRACTION100
3.3664-4.240.16781470.14081417X-RAY DIFFRACTION100
4.24-33.30060.17361660.12981506X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.0799 Å / Origin y: 3.0163 Å / Origin z: -49.9174 Å
111213212223313233
T0.1165 Å2-0.001 Å2-0.0208 Å2-0.1902 Å2-0.0228 Å2--0.1609 Å2
L3.7852 °20.6323 °2-0.7496 °2-2.789 °20.3056 °2--1.9824 °2
S-0.0425 Å °-0.1458 Å °0.3591 Å °0.0265 Å °0.0917 Å °0.1297 Å °0.0545 Å °-0.0855 Å °-0.0277 Å °
Refinement TLS groupSelection details: chain 'A' and resid 5 through 190

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