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- PDB-5i0s: Thiosulfate bound Cysteine Dioxygenase at pH 6.2 -

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Basic information

Entry
Database: PDB / ID: 5i0s
TitleThiosulfate bound Cysteine Dioxygenase at pH 6.2
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / cupin-fold / cysteine to cysteine sulfinate / C93-Y157 crosslink / catalysis oxidation / thiosulfate
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
: / THIOSULFATE / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKean, K.M. / Driggers, C.M. / Karplus, P.A.
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
DepositionFeb 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 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 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2593
Polymers23,0911
Non-polymers1682
Water5,891327
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

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Components

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


Mass: 23090.953 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


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


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M tri-sodium citrate pH 5.6, 24% PEG 4000, 0.15 M ammonium acetate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.3→33.93 Å / Num. obs: 51666 / % possible obs: 99.9 % / Redundancy: 25.7 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 16.7
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 0.7 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIO

4eio
PDB Unreleased entry


Resolution: 1.3→33.907 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 5034 9.8 %
Rwork0.1741 --
obs0.1768 51392 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→33.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 6 327 1839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011688
X-RAY DIFFRACTIONf_angle_d1.0122303
X-RAY DIFFRACTIONf_dihedral_angle_d14.368633
X-RAY DIFFRACTIONf_chiral_restr0.08242
X-RAY DIFFRACTIONf_plane_restr0.006306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.3391410.32151475X-RAY DIFFRACTION94
1.3148-1.33030.33081480.31861493X-RAY DIFFRACTION99
1.3303-1.34650.32381550.29951518X-RAY DIFFRACTION100
1.3465-1.36350.33841920.29561492X-RAY DIFFRACTION100
1.3635-1.38150.31341590.28881524X-RAY DIFFRACTION100
1.3815-1.40040.31081740.2661536X-RAY DIFFRACTION100
1.4004-1.42040.30181450.27261519X-RAY DIFFRACTION100
1.4204-1.44160.28261850.24971538X-RAY DIFFRACTION100
1.4416-1.46420.24361580.21881500X-RAY DIFFRACTION100
1.4642-1.48820.2241750.21641520X-RAY DIFFRACTION100
1.4882-1.51380.24881760.20351551X-RAY DIFFRACTION100
1.5138-1.54130.23821450.19351516X-RAY DIFFRACTION100
1.5413-1.5710.20871820.18681537X-RAY DIFFRACTION100
1.571-1.60310.20351850.17791501X-RAY DIFFRACTION100
1.6031-1.63790.19181500.17381556X-RAY DIFFRACTION100
1.6379-1.6760.20621750.16231517X-RAY DIFFRACTION100
1.676-1.71790.19611730.17161531X-RAY DIFFRACTION100
1.7179-1.76440.20361630.16711541X-RAY DIFFRACTION100
1.7644-1.81630.19261590.15961557X-RAY DIFFRACTION100
1.8163-1.87490.20021590.16771551X-RAY DIFFRACTION100
1.8749-1.94190.20571530.17971568X-RAY DIFFRACTION100
1.9419-2.01970.18851840.15861533X-RAY DIFFRACTION100
2.0197-2.11160.17571830.14981542X-RAY DIFFRACTION100
2.1116-2.22290.18841550.15971579X-RAY DIFFRACTION100
2.2229-2.36210.2121650.1691548X-RAY DIFFRACTION100
2.3621-2.54440.18411630.15351596X-RAY DIFFRACTION100
2.5444-2.80040.20181880.15591561X-RAY DIFFRACTION100
2.8004-3.20530.18251820.15941596X-RAY DIFFRACTION100
3.2053-4.03730.17661750.15251614X-RAY DIFFRACTION100
4.0373-33.91840.18071870.16911748X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.117 Å / Origin y: 2.9669 Å / Origin z: -49.981 Å
111213212223313233
T0.1012 Å2-0.002 Å2-0.0029 Å2-0.1122 Å20.0064 Å2--0.1161 Å2
L0.6077 °20.2679 °2-0.1886 °2-0.6463 °2-0.048 °2--0.616 °2
S-0.0077 Å °0.0018 Å °-0.0472 Å °0.0149 Å °0.0126 Å °0.0012 Å °0.0586 Å °-0.0321 Å °-0.0001 Å °
Refinement TLS groupSelection details: chain 'A' and resid 5 through 190

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