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- PDB-4pix: Unliganded Cysteine Dioxygenase C93A variant at pH 6.2 -

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Basic information

Entry
Database: PDB / ID: 4pix
TitleUnliganded Cysteine Dioxygenase C93A variant at pH 6.2
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 / Resolution: 1.35 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

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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)23,1183
Polymers23,0271
Non-polymers912
Water4,576254
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 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: Apr 22, 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: 1.35→39 Å / Num. all: 40379 / Num. obs: 40379 / % possible obs: 86.2 % / Redundancy: 23.4 % / Net I/σ(I): 12.7
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 0.6 / % possible all: 76.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.35→33.907 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 3880 9.81 %
Rwork0.1727 --
obs0.176 39568 85.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→33.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 2 254 1761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131627
X-RAY DIFFRACTIONf_angle_d1.3062213
X-RAY DIFFRACTIONf_dihedral_angle_d13.288613
X-RAY DIFFRACTIONf_chiral_restr0.08236
X-RAY DIFFRACTIONf_plane_restr0.007292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36650.349790.373661X-RAY DIFFRACTION62
1.3665-1.38380.3477790.3509780X-RAY DIFFRACTION81
1.3838-1.4020.35091530.34341440X-RAY DIFFRACTION98
1.402-1.42120.34141410.32011446X-RAY DIFFRACTION100
1.4212-1.44150.29531010.3165905X-RAY DIFFRACTION81
1.4415-1.4630.36791330.30131272X-RAY DIFFRACTION89
1.463-1.48590.277910.2604856X-RAY DIFFRACTION59
1.4859-1.51020.33031530.24081469X-RAY DIFFRACTION100
1.5102-1.53630.23531120.2292915X-RAY DIFFRACTION63
1.5363-1.56420.22661600.19821460X-RAY DIFFRACTION100
1.5642-1.59430.2181670.19111454X-RAY DIFFRACTION100
1.5943-1.62680.20241590.19031468X-RAY DIFFRACTION100
1.6268-1.66220.21051710.18151458X-RAY DIFFRACTION100
1.6622-1.70090.2221630.18021472X-RAY DIFFRACTION100
1.7009-1.74340.19741270.17941113X-RAY DIFFRACTION76
1.7434-1.79050.20651570.18081465X-RAY DIFFRACTION100
1.7905-1.84320.23671460.16611501X-RAY DIFFRACTION100
1.8432-1.90270.20921290.17221227X-RAY DIFFRACTION84
1.9027-1.97070.2169960.1657854X-RAY DIFFRACTION58
1.9707-2.04960.19281780.15961486X-RAY DIFFRACTION100
2.0496-2.14290.19051320.161162X-RAY DIFFRACTION78
2.1429-2.25580.22171170.15371139X-RAY DIFFRACTION77
2.2558-2.39710.19661480.16241518X-RAY DIFFRACTION99
2.3971-2.58220.2251670.16881495X-RAY DIFFRACTION100
2.5822-2.84190.22971380.17091253X-RAY DIFFRACTION83
2.8419-3.25280.18711710.1681529X-RAY DIFFRACTION100
3.2528-4.09710.18511310.14391227X-RAY DIFFRACTION78
4.0971-33.91760.16671810.15091663X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.3382 Å / Origin y: 3.0623 Å / Origin z: -49.8696 Å
111213212223313233
T0.0864 Å20.0029 Å2-0.0063 Å2-0.1093 Å20.0109 Å2--0.1015 Å2
L1.3773 °20.4698 °2-0.2293 °2-1.7586 °20.1982 °2--1.5883 °2
S-0.002 Å °-0.0138 Å °-0.0387 Å °0.056 Å °-0.002 Å °0.036 Å °0.0941 Å °-0.0549 Å °-0.002 Å °
Refinement TLS groupSelection details: chain 'A' and resid 5 through 190

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