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- PDB-4xfb: cysteine dioxygenase variant - C93A at pH 8.0 unliganded -

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Basic information

Entry
Database: PDB / ID: 4xfb
Titlecysteine dioxygenase variant - C93A at pH 8.0 unliganded
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 / 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
: / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / 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)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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water5,999333
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
Components on special symmetry positions
IDModelComponents
11A-882-

HOH

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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.: 333 / 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 growMethod: 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

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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: 1.35→41 Å / Num. all: 45533 / Num. obs: 45445 / % possible obs: 97.9 % / Redundancy: 23.3 % / Net I/σ(I): 22.5
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 1 / % possible all: 78.6

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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: 1.35→40.729 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 4493 9.89 %same 5% as 4ieu
Rwork0.161 ---
obs0.164 45445 97.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→40.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 2 333 1840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141677
X-RAY DIFFRACTIONf_angle_d1.3022284
X-RAY DIFFRACTIONf_dihedral_angle_d14.218633
X-RAY DIFFRACTIONf_chiral_restr0.083240
X-RAY DIFFRACTIONf_plane_restr0.006305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3459-1.36120.38041140.3478991X-RAY DIFFRACTION73
1.3612-1.37720.35071270.31641114X-RAY DIFFRACTION81
1.3772-1.3940.29391240.29771185X-RAY DIFFRACTION87
1.394-1.41170.30111450.28521293X-RAY DIFFRACTION92
1.4117-1.43020.30231260.2461319X-RAY DIFFRACTION96
1.4302-1.44980.28491580.24411340X-RAY DIFFRACTION99
1.4498-1.47050.22171580.21941384X-RAY DIFFRACTION100
1.4705-1.49250.22621440.19851367X-RAY DIFFRACTION100
1.4925-1.51580.231660.19171381X-RAY DIFFRACTION100
1.5158-1.54070.21751490.17411344X-RAY DIFFRACTION100
1.5407-1.56720.21791700.17651382X-RAY DIFFRACTION100
1.5672-1.59570.21921550.1551378X-RAY DIFFRACTION100
1.5957-1.62640.15791390.15671386X-RAY DIFFRACTION100
1.6264-1.65960.17981560.15661365X-RAY DIFFRACTION100
1.6596-1.69570.19551530.15721417X-RAY DIFFRACTION100
1.6957-1.73520.17621590.15561366X-RAY DIFFRACTION100
1.7352-1.77860.18651530.16261373X-RAY DIFFRACTION100
1.7786-1.82660.21141340.15141403X-RAY DIFFRACTION100
1.8266-1.88040.17421360.151408X-RAY DIFFRACTION100
1.8804-1.94110.20811430.15481417X-RAY DIFFRACTION100
1.9411-2.01050.17521680.15231368X-RAY DIFFRACTION100
2.0105-2.09090.18041720.15221379X-RAY DIFFRACTION100
2.0909-2.18610.16741380.14261423X-RAY DIFFRACTION100
2.1861-2.30140.17171450.14181433X-RAY DIFFRACTION100
2.3014-2.44550.18581440.14961403X-RAY DIFFRACTION100
2.4455-2.63430.18611620.15641426X-RAY DIFFRACTION100
2.6343-2.89930.20051680.15911417X-RAY DIFFRACTION100
2.8993-3.31870.18411590.15361432X-RAY DIFFRACTION100
3.3187-4.18060.17241590.14541478X-RAY DIFFRACTION100
4.1806-40.7480.16811690.1481580X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.156 Å / Origin y: 3.0762 Å / Origin z: -49.5263 Å
111213212223313233
T0.0489 Å2-0.001 Å2-0.0022 Å2-0.0647 Å20.0017 Å2--0.0603 Å2
L0.8362 °20.4115 °2-0.1688 °2-0.7547 °20.0786 °2--0.7024 °2
S0.0224 Å °-0.0242 Å °-0.0239 Å °0.0259 Å °-0.0205 Å °-0.0073 Å °0.046 Å °-0.0248 Å °0.0406 Å °
Refinement TLS groupSelection details: chain 'A' and resid 5 through 190

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