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- PDB-4ubg: Resting state of rat cysteine dioxygenase C93G variant -

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Basic information

Entry
Database: PDB / ID: 4ubg
TitleResting state of rat cysteine dioxygenase C93G variant
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / cysteine dioxygenase / non-heme mono-iron / Cupin / cysteine to glycine substitution
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
: / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
Model detailsC93G variant
AuthorsFellner, M. / Tchesnokov, E.P. / Jameson, G.N. / Wilbanks, S.M.
CitationJournal: Biochemistry / Year: 2014
Title: The Cys-Tyr Cross-Link of Cysteine Dioxygenase Changes the Optimal pH of the Reaction without a Structural Change.
Authors: Davies, C.G. / Fellner, M. / Tchesnokov, E.P. / Wilbanks, S.M. / Jameson, G.N.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Jan 14, 2015Group: Database references
Revision 1.4Feb 4, 2015Group: Derived calculations
Revision 1.5Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Sep 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_conn_angle / refine_hist / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)24,47611
Polymers24,2131
Non-polymers26310
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.840, 57.840, 122.730
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: 24213.104 Da / Num. of mol.: 1 / Mutation: C93G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Plasmid: pPR-IBA1/RatCDO/C93GFVariant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: Hanging drops of 1.5 microL of approximately 7 mg/mL C93G-CDO (10mM sodiumphosphate, 20mM NaCl pH 7.5) and 0.6 microL wt-CDO seeds in their own growth solution (25% (w/v) polyethylene glycol ...Details: Hanging drops of 1.5 microL of approximately 7 mg/mL C93G-CDO (10mM sodiumphosphate, 20mM NaCl pH 7.5) and 0.6 microL wt-CDO seeds in their own growth solution (25% (w/v) polyethylene glycol 1500, 13mM succinate, 44mM sodiumphosphate, 44mM glycine) and 1.5 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (26% (w/v) polyethylene glycol 4000, 200 mM ammonium acetate, 100 mM sodium citrate).

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.82→52.32 Å / Num. obs: 17317 / % possible obs: 88.3 % / Redundancy: 13.4 % / Biso Wilson estimate: 16.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.036 / Net I/σ(I): 16.8 / Num. measured all: 232626 / Scaling rejects: 767
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.82-1.8612.91.2461.91458111310.8190.359100
9.09-52.329.40.03142.819762110.9990.0199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
Aimless0.3.5data scaling
PDB_EXTRACT3.14data extraction
MOSFLM7.1.0data reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kwj

4kwj


Resolution: 1.9→42.1004 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2414 --
Rwork0.2019 --
obs-14449 89.1 %
Displacement parametersBiso max: 95.26 Å2 / Biso mean: 22.2998 Å2 / Biso min: 4.92 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.1004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 10 215 1742

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