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- PDB-5fdb: Iron free rat cysteine dioxygenase R60QC164R variant -

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Basic information

Entry
Database: PDB / ID: 5fdb
TitleIron free rat cysteine dioxygenase R60QC164R variant
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / thioether bond / post-translational modification / post translational / posttranslational / cysteine dioxygenase / iron / non-heme mono-iron / cupin / arginine to glutamine substitution / cysteine to arginine substitution / beta barrel
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
Model detailsR60QC164R variant
AuthorsFellner, M. / Davies, C.G. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M.
CitationJournal: To be published
Title: Iron free rat cysteine dioxygenase R60QC164R variant
Authors: Wilbanks, S.M.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine dioxygenase type 1


Theoretical massNumber of molelcules
Total (without water)23,0841
Polymers23,0841
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.190, 57.190, 123.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

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Components

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


Mass: 23083.875 Da / Num. of mol.: 1 / Mutation: R60Q,C164R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Plasmid: pPR-IBA1/RatCDO/R60QC164R_Variant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P21816, cysteine dioxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Hanging drops of 1 uL of 31.7 mg/mL R60QC164R CDO which had been iron reconstituted to 57% occupancy [100mM Tris-HCl, 50mM NaCl pH 8.0] and 2 uL of reservoir buffer containing crushed WT CDO ...Details: Hanging drops of 1 uL of 31.7 mg/mL R60QC164R CDO which had been iron reconstituted to 57% occupancy [100mM Tris-HCl, 50mM NaCl pH 8.0] and 2 uL of reservoir buffer containing crushed WT CDO seeds were allowed to equilibrate above the reservoir buffer [26% (w/v) polyethylene glycol 4000, 200 mM ammonium acetate, and 100 mM sodium citrate (pH 6.2)].

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→57.19 Å / Num. obs: 21417 / % possible obs: 99.9 % / Redundancy: 11.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.03 / Net I/σ(I): 14.5 / Num. measured all: 244273 / Scaling rejects: 2831
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.75-1.796.20.4652.2765912400.8990.20299.3
8.75-57.1990.04724.119912220.9980.01696.2

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Processing

Software
NameVersionClassification
MOSFLM7.1.0data reduction
Aimless0.3.11data scaling
PHASER2.6.0phasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KWJ

4kwj


Resolution: 1.75→33.796 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 2001 5.1 %
Rwork0.1888 37239 -
obs0.1903 39240 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.95 Å2 / Biso mean: 22.5136 Å2 / Biso min: 4.98 Å2
Refinement stepCycle: final / Resolution: 1.75→33.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 0 180 1702
Biso mean---34.32 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071600
X-RAY DIFFRACTIONf_angle_d0.7932171
X-RAY DIFFRACTIONf_chiral_restr0.054232
X-RAY DIFFRACTIONf_plane_restr0.005284
X-RAY DIFFRACTIONf_dihedral_angle_d13.535952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.79380.2721660.25312619278598
1.7938-1.84230.26131300.223226672797100
1.8423-1.89650.29461300.221826432773100
1.8965-1.95770.27871490.287926762825100
1.9577-2.02770.23281490.188526512800100
2.0277-2.10880.23571410.225426622803100
2.1088-2.20480.22041440.166326812825100
2.2048-2.3210.23171360.218626402776100
2.321-2.46640.23361470.185526842831100
2.4664-2.65680.24731810.192726112792100
2.6568-2.9240.1961510.187826502801100
2.924-3.34680.19091330.169426982831100
3.3468-4.21530.15361260.150726772803100
4.2153-33.8020.20941180.170226802798100

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