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- PDB-4yni: Iron free succinate bound rat cysteine dioxygenase -

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Basic information

Entry
Database: PDB / ID: 4yni
TitleIron free succinate bound rat cysteine dioxygenase
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / non-heme mono-iron / Cupin / succinate / iron free
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
SUCCINIC ACID / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.404 Å
AuthorsFellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M.
CitationJournal: To be published
Title: Iron free succinate bound rat cysteine dioxygenase
Authors: Fellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)24,4003
Polymers24,2591
Non-polymers1412
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.690, 57.690, 121.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 24259.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Plasmid: pPR-IBA1/RatCDO/WT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P21816, cysteine dioxygenase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Hanging drops of 1 microL of 15 mg/mL WT-CDO (10mM sodiumphosphate, 20mM NaCl pH 7.5) and 3 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (25% (w/v) ...Details: Hanging drops of 1 microL of 15 mg/mL WT-CDO (10mM sodiumphosphate, 20mM NaCl pH 7.5) and 3 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (25% (w/v) polyethylene glycol 1500, 13 mM succinate, 44 mM mono sodium phosphate, 44 mM glycine) and 0.6 microL WT-CDO seeds (grown in the reservoir buffer)

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 2, 2013 / Details: Osmic VariMax optics
RadiationMonochromator: Osmic VariMax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.4→41.89 Å / Num. obs: 15515 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 36.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.044 / Net I/σ(I): 11.5 / Num. measured all: 85493 / Scaling rejects: 168
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
2.4-2.498.60.7563.672668470.8680.275100
9-41.897.60.06117.116392150.9950.02299.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLM7.1.0data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KWJ

4kwj


Resolution: 2.404→41.89 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 779 5.14 %Random selection
Rwork0.175 14390 --
obs0.1776 15169 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.03 Å2 / Biso mean: 39.297 Å2 / Biso min: 20.93 Å2
Refinement stepCycle: final / Resolution: 2.404→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 9 87 1615
Biso mean--45.65 41.16 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011602
X-RAY DIFFRACTIONf_angle_d1.0682171
X-RAY DIFFRACTIONf_chiral_restr0.058230
X-RAY DIFFRACTIONf_plane_restr0.005285
X-RAY DIFFRACTIONf_dihedral_angle_d13.542593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.404-2.55470.30711450.242423522497100
2.5547-2.75190.31271290.226824262555100
2.7519-3.02880.30291140.209724302544100
3.0288-3.46690.24351110.18972409252099
3.4669-4.36720.2151550.15662359251499
4.3672-41.89960.1441250.13612414253999

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