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- PDB-4piy: Homocysteine bound Cysteine Dioxygenase C93A variant at pH 6.2 -

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Basic information

Entry
Database: PDB / ID: 4piy
TitleHomocysteine bound Cysteine Dioxygenase C93A variant at pH 6.2
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
: / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 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)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
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 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 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)23,2183
Polymers23,0271
Non-polymers1912
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
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-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine / Homocysteine


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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 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: 5.0.2 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2013
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) LIQUID N2 COOLED / 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: 28457 / % possible obs: 99.6 % / Redundancy: 13.8 % / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 1.1 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.6→40.729 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 2721 9.78 %
Rwork0.1643 --
obs0.1687 27819 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→40.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 9 279 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121630
X-RAY DIFFRACTIONf_angle_d1.2772218
X-RAY DIFFRACTIONf_dihedral_angle_d13.713612
X-RAY DIFFRACTIONf_chiral_restr0.054237
X-RAY DIFFRACTIONf_plane_restr0.006293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62910.3151220.29751284X-RAY DIFFRACTION98
1.6291-1.66040.31891530.27291250X-RAY DIFFRACTION99
1.6604-1.69430.29361490.26761301X-RAY DIFFRACTION99
1.6943-1.73120.28351530.25171256X-RAY DIFFRACTION99
1.7312-1.77140.28981240.26071308X-RAY DIFFRACTION99
1.7714-1.81570.27761310.2181306X-RAY DIFFRACTION99
1.8157-1.86480.24651300.19681295X-RAY DIFFRACTION99
1.8648-1.91970.2431310.18151314X-RAY DIFFRACTION99
1.9197-1.98170.2221440.17671314X-RAY DIFFRACTION99
1.9817-2.05250.21661550.16491281X-RAY DIFFRACTION99
2.0525-2.13470.18161490.15761317X-RAY DIFFRACTION100
2.1347-2.23180.21841320.15281313X-RAY DIFFRACTION99
2.2318-2.34950.19731390.1511318X-RAY DIFFRACTION100
2.3495-2.49660.2191370.1541344X-RAY DIFFRACTION100
2.4966-2.68940.22881690.1551307X-RAY DIFFRACTION100
2.6894-2.95990.22841400.15951350X-RAY DIFFRACTION100
2.9599-3.38810.18441540.15211372X-RAY DIFFRACTION100
3.3881-4.26790.18661430.13391380X-RAY DIFFRACTION100
4.2679-40.74250.16281660.14471488X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.206 Å / Origin y: 3.0286 Å / Origin z: -49.8693 Å
111213212223313233
T0.0921 Å20.0029 Å2-0.0049 Å2-0.1169 Å20.0128 Å2--0.1092 Å2
L1.481 °20.6099 °2-0.2781 °2-2.0153 °20.1503 °2--1.5902 °2
S-0.0101 Å °-0.0187 Å °-0.03 Å °0.0538 Å °0.0092 Å °0.0613 Å °0.095 Å °-0.0891 Å °-0.0012 Å °
Refinement TLS groupSelection details: chain 'A' and resid 5 through 190

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