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- PDB-6u4s: wild type cysteine dioxygenase -

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Basic information

Entry
Database: PDB / ID: 6u4s
Titlewild type cysteine dioxygenase
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / non-heme / dioxygenase / cysteine-tyrosine crosslink
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
: / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMeneely, K.M. / Chilton, A.S. / Forbes, D.L. / Ellis, H.R. / Lamb, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1403293 United States
CitationJournal: Biochemistry / Year: 2020
Title: The 3-His Metal Coordination Site Promotes the Coupling of Oxygen Activation to Cysteine Oxidation in Cysteine Dioxygenase.
Authors: Forbes, D.L. / Meneely, K.M. / Chilton, A.S. / Lamb, A.L. / Ellis, H.R.
History
DepositionAug 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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)23,1012
Polymers23,0451
Non-polymers561
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.454, 57.454, 122.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Cysteine dioxygenase type 1 / / Cysteine dioxygenase type I / CDO-I


Mass: 23044.863 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 5.5, 1 M lithium chloride, 22.5% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→38.55 Å / Num. obs: 7638 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 36.94 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.5
Reflection shellResolution: 2.49→2.59 Å / Num. unique obs: 809 / CC1/2: 0.901

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B5H

2b5h


Resolution: 2.49→38.55 Å / SU ML: 0.3721 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9926
RfactorNum. reflection% reflection
Rfree0.2617 760 10 %
Rwork0.1854 --
obs0.1927 7599 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.82 Å2
Refinement stepCycle: LAST / Resolution: 2.49→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 1 5 1508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01361540
X-RAY DIFFRACTIONf_angle_d1.45672084
X-RAY DIFFRACTIONf_chiral_restr0.0562223
X-RAY DIFFRACTIONf_plane_restr0.0095271
X-RAY DIFFRACTIONf_dihedral_angle_d3.8201915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.680.33861450.25061307X-RAY DIFFRACTION97.84
2.68-2.950.31541490.21261336X-RAY DIFFRACTION99.46
2.95-3.380.29241510.20891356X-RAY DIFFRACTION98.69
3.38-4.260.24321510.16151372X-RAY DIFFRACTION100

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