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- PDB-4kwl: Rat cysteine dioxygenase with 3-mercaptopropionic acid persulfide... -

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Basic information

Entry
Database: PDB / ID: 4kwl
TitleRat cysteine dioxygenase with 3-mercaptopropionic acid persulfide bound
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / non-heme / mono-iron / cupin / 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
3-disulfanylpropanoic acid / : / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSouness, R.J. / Wilbanks, S.M. / Jameson, G.B. / Jameson, G.N.L.
CitationJournal: Biochemistry / Year: 2013
Title: Mechanistic implications of persulfenate and persulfide binding in the active site of cysteine dioxygenase.
Authors: Souness, R.J. / Kleffmann, T. / Tchesnokov, E.P. / Wilbanks, S.M. / Jameson, G.B. / Jameson, G.N.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)23,2533
Polymers23,0591
Non-polymers1942
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)57.560, 57.560, 122.000
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 / CDO-I


Mass: 23058.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Plasmid: rCDO/pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21816, cysteine dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-3SS / 3-disulfanylpropanoic acid


Mass: 138.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2S2
#4: Water ChemComp-HOH / water / Water


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

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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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Hanging drops of 1.5 microL of approximately 8 mg/mL CDO and 1.5 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (24-34% (w/v) polyethylene glycol 4000, 100- ...Details: Hanging drops of 1.5 microL of approximately 8 mg/mL CDO and 1.5 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (24-34% (w/v) polyethylene glycol 4000, 100-250 mM ammonium acetate, 100 mM sodium citrate, 0-4 mM dithionite, 40 mM 3-mercaptopropionic acid). Crystals grew as needles or starbursts of approximately 0.1 mm in length in one week, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 31, 2012 / Details: Double Si with sagittaly bent second crystal
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.63→52.06 Å / Num. all: 26441 / Num. obs: 26441 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 5.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 296.1
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 27.2 / Num. unique all: 3769 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Ice(McPhillipsdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3eln

3eln


Resolution: 1.63→30.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.07 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1312 5.1 %The same R-free flags as PDB 3eln
Rwork0.20966 ---
obs0.21095 24606 98.22 %-
all-26368 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å2-0 Å2
2---0.24 Å2-0 Å2
3---0.49 Å2
Refine analyzeLuzzati coordinate error obs: 0.2157 Å
Refinement stepCycle: LAST / Resolution: 1.63→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 8 180 1707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021615
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9342196
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92924.16784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69515277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.794159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211256
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 77 -
Rwork0.33 1550 -
obs-1550 94.05 %

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