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- PDB-4xez: cysteine dioxygenase variant - Y157F at pH 8.0 with dithionite -

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Basic information

Entry
Database: PDB / ID: 4xez
Titlecysteine dioxygenase variant - Y157F at pH 8.0 with dithionite
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cupin Fold / cysteine to cysteine sulfinic acid catalysis / Cytosol / thiol dioxygenase
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 / FOURIER SYNTHESIS / Resolution: 1.2469 Å
AuthorsDriggers, C.M. / Karplus, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)NIH-DK-056649 United States
Department of Energy (DOE, United States)DE-AC02-98CH10886 United States
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
DepositionDec 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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

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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)23,2464
Polymers23,0431
Non-polymers2033
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-33 kcal/mol
Surface area9350 Å2
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
Components on special symmetry positions
IDModelComponents
11A-882-

HOH

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Components

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


Mass: 23042.889 Da / Num. of mol.: 1 / Mutation: Y157F
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-THJ / THIOSULFATE


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


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M tri-sodium citrate pH=5.6, 24% PEG 4000, 0.15M ammonium acetate. 1:1 drop ratio with microseeding.; Soak solution at pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2014
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.2469→26 Å / Num. all: 53790 / Num. obs: 53704 / % possible obs: 92.3 % / Redundancy: 22.2 % / Net I/σ(I): 27.1
Reflection shellResolution: 1.2469→1.27 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.4 / % possible all: 45.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIX(phenix.refine: 1.9_1692)phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ieu

4ieu


Resolution: 1.2469→26 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1617 5308 9.88 %same 5% as 4ieu
Rwork0.1209 ---
obs0.1249 53704 92.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2469→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 7 354 1866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111633
X-RAY DIFFRACTIONf_angle_d1.2452218
X-RAY DIFFRACTIONf_dihedral_angle_d12.895607
X-RAY DIFFRACTIONf_chiral_restr0.078237
X-RAY DIFFRACTIONf_plane_restr0.006292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2469-1.26110.2885960.2508696X-RAY DIFFRACTION42
1.2611-1.2760.29451020.2272889X-RAY DIFFRACTION51
1.276-1.29150.2327920.21891049X-RAY DIFFRACTION60
1.2915-1.30790.22121380.18781172X-RAY DIFFRACTION69
1.3079-1.32510.21751400.17291304X-RAY DIFFRACTION76
1.3251-1.34320.22341430.17781455X-RAY DIFFRACTION83
1.3432-1.36240.22341850.16021488X-RAY DIFFRACTION88
1.3624-1.38270.20041840.15461623X-RAY DIFFRACTION94
1.3827-1.40440.20971820.1521711X-RAY DIFFRACTION98
1.4044-1.42740.1921680.13811736X-RAY DIFFRACTION100
1.4274-1.4520.17471920.1231717X-RAY DIFFRACTION100
1.452-1.47840.17182020.11781730X-RAY DIFFRACTION100
1.4784-1.50680.15931870.10951725X-RAY DIFFRACTION100
1.5068-1.53760.15931980.09841717X-RAY DIFFRACTION100
1.5376-1.5710.14592090.10261730X-RAY DIFFRACTION100
1.571-1.60750.13781990.09781716X-RAY DIFFRACTION100
1.6075-1.64770.12271760.10041766X-RAY DIFFRACTION100
1.6477-1.69230.14011930.10091732X-RAY DIFFRACTION100
1.6923-1.74210.15171920.1081734X-RAY DIFFRACTION100
1.7421-1.79830.13281870.11241752X-RAY DIFFRACTION100
1.7983-1.86250.15911750.10791766X-RAY DIFFRACTION100
1.8625-1.93710.15351770.10771758X-RAY DIFFRACTION100
1.9371-2.02520.14972030.10191742X-RAY DIFFRACTION100
2.0252-2.13190.13082000.11071755X-RAY DIFFRACTION100
2.1319-2.26540.13531920.10731780X-RAY DIFFRACTION100
2.2654-2.44020.15661740.12051786X-RAY DIFFRACTION100
2.4402-2.68560.1872160.1251759X-RAY DIFFRACTION100
2.6856-3.07370.16521970.13121818X-RAY DIFFRACTION100
3.0737-3.87050.16521980.11841839X-RAY DIFFRACTION100
3.8705-26.06450.15962110.12621951X-RAY DIFFRACTION100

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