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- PDB-4xfg: cysteine dioxygenase variant - C93A at pH 6.2 with cysteine -

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Basic information

Entry
Database: PDB / ID: 4xfg
Titlecysteine dioxygenase variant - C93A at pH 6.2 with cysteine
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cupin Fold / cysteine to cysteine sulfinic acid catalysis / 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
CYSTEINE / : / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.401 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 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 20, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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)23,2394
Polymers23,0271
Non-polymers2123
Water5,386299
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
Components on special symmetry positions
IDModelComponents
11A-698-

HOH

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Components

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


Mass: 23026.822 Da / Num. of mol.: 1 / Mutation: C93A
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-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %
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 6.2

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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: 1.4→34 Å / Num. all: 41405 / Num. obs: 41323 / % possible obs: 100 % / Redundancy: 23.7 % / Net I/σ(I): 11.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ieu

4ieu


Resolution: 1.401→33.907 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 4073 9.86 %same 5% as 4ieu
Rwork0.163 ---
obs0.1663 41323 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.401→33.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 9 299 1810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151624
X-RAY DIFFRACTIONf_angle_d1.2762206
X-RAY DIFFRACTIONf_dihedral_angle_d12.799610
X-RAY DIFFRACTIONf_chiral_restr0.08236
X-RAY DIFFRACTIONf_plane_restr0.006290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.401-1.41750.37481160.34611230X-RAY DIFFRACTION98
1.4175-1.43480.3251460.33211271X-RAY DIFFRACTION100
1.4348-1.4530.31111290.30711264X-RAY DIFFRACTION100
1.453-1.47210.3251520.29561245X-RAY DIFFRACTION100
1.4721-1.49230.27651310.27351266X-RAY DIFFRACTION100
1.4923-1.51360.26431570.24641267X-RAY DIFFRACTION100
1.5136-1.53620.24461350.21761253X-RAY DIFFRACTION100
1.5362-1.56020.25291480.21281244X-RAY DIFFRACTION100
1.5602-1.58580.20251480.19841247X-RAY DIFFRACTION100
1.5858-1.61310.1971450.19041269X-RAY DIFFRACTION100
1.6131-1.64240.21471210.17951280X-RAY DIFFRACTION100
1.6424-1.6740.21831450.17861277X-RAY DIFFRACTION100
1.674-1.70820.21021410.16611258X-RAY DIFFRACTION100
1.7082-1.74530.19631410.16751276X-RAY DIFFRACTION100
1.7453-1.78590.20391390.16221270X-RAY DIFFRACTION100
1.7859-1.83060.19221320.15781269X-RAY DIFFRACTION100
1.8306-1.88010.17721190.1571296X-RAY DIFFRACTION100
1.8801-1.93540.211310.16211299X-RAY DIFFRACTION100
1.9354-1.99790.19361530.14671270X-RAY DIFFRACTION100
1.9979-2.06920.19741550.16411265X-RAY DIFFRACTION100
2.0692-2.15210.16951370.14521292X-RAY DIFFRACTION100
2.1521-2.250.2131290.15281299X-RAY DIFFRACTION100
2.25-2.36860.18481380.15031299X-RAY DIFFRACTION100
2.3686-2.5170.19721290.15341306X-RAY DIFFRACTION100
2.517-2.71120.21581670.15391288X-RAY DIFFRACTION100
2.7112-2.98390.20011350.16541313X-RAY DIFFRACTION100
2.9839-3.41540.18331520.14581335X-RAY DIFFRACTION100
3.4154-4.30160.16211400.13051356X-RAY DIFFRACTION100
4.3016-33.91680.15591620.14051446X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.2465 Å / Origin y: 2.9767 Å / Origin z: -49.8906 Å
111213212223313233
T0.0823 Å2-0.004 Å2-0.0021 Å2-0.0965 Å20.0048 Å2--0.0911 Å2
L0.7375 °20.2321 °2-0.2105 °2-0.7058 °2-0.0162 °2--0.7559 °2
S-0.0005 Å °0.0049 Å °-0.022 Å °0.0092 Å °0.0075 Å °-0.0117 Å °0.0457 Å °-0.0282 Å °-0.0004 Å °
Refinement TLS groupSelection details: chain 'A' and resid 5 through 190

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