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- PDB-5efu: Resting state of rat cysteine dioxygenase H155Q variant -

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Basic information

Entry
Database: PDB / ID: 5efu
TitleResting state of rat cysteine dioxygenase H155Q variant
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / cysteine dioxygenase / non-heme mono-iron / Cupin / histidine to glutamine 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 / Resolution: 2.8 Å
Model detailsH155Q variant
AuthorsFellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M.
CitationJournal: To be published
Title: Resting state of rat cysteine dioxygenase H155Q variant
Authors: Fellner, M. / Wilbanks, S.M.
History
DepositionOct 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 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 / diffrn_radiation_wavelength / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine dioxygenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3052
Polymers24,2491
Non-polymers561
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.610, 57.610, 119.510
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: 24249.178 Da / Num. of mol.: 1 / Mutation: H155Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Plasmid: pPR-IBA1/RatCDO/H155Q_Variant / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Hanging drops of 2.5 microL of approximately 25 mg/mL H155Q-CDO (10 mM sodiumphosphate, 20 mM NaCl pH 7.5) and 2.5 microL reservoir buffer containg H155Q-CDO crushed seeds were allowed to ...Details: Hanging drops of 2.5 microL of approximately 25 mg/mL H155Q-CDO (10 mM sodiumphosphate, 20 mM NaCl pH 7.5) and 2.5 microL reservoir buffer containg H155Q-CDO crushed seeds 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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→57.61 Å / Num. obs: 5403 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 47 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Net I/σ(I): 14.1 / Num. measured all: 35296 / Scaling rejects: 238
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
2.8-2.996.80.4254.664929480.9180.176100
7.92-57.615.30.0424.414782790.9980.01898.4

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Processing

Software
NameVersionClassification
MOSFLM7.1.0data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KWJ

4kwj


Resolution: 2.8→28.805 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 461 4.88 %
Rwork0.1817 8995 -
obs0.1845 9456 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.97 Å2 / Biso mean: 45.7557 Å2 / Biso min: 14.56 Å2
Refinement stepCycle: final / Resolution: 2.8→28.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 1 4 1523
Biso mean--45.77 41.61 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141581
X-RAY DIFFRACTIONf_angle_d1.0662136
X-RAY DIFFRACTIONf_chiral_restr0.057228
X-RAY DIFFRACTIONf_plane_restr0.005279
X-RAY DIFFRACTIONf_dihedral_angle_d15.866581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8003-3.20510.37261550.249130193174
3.2051-4.03630.22921550.18529753130
4.0363-28.80650.19931510.153630013152

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