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- PDB-6u1m: Resting state of rat cysteine dioxygenase R60E variant -

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Basic information

Entry
Database: PDB / ID: 6u1m
TitleResting state of rat cysteine dioxygenase R60E variant
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / cysteine / b-barrel / R60E / arginine mutation / octahedral
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 dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsPinkney, H.R. / Fellner, M. / Wilbanks, S.M.
CitationJournal: To be Published
Title: Resting state of rat cysteine dioxygenase R60E variant
Authors: Fellner, M.
History
DepositionAug 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)23,0872
Polymers23,0311
Non-polymers561
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-14 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.546, 57.546, 121.624
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: 23030.809 Da / Num. of mol.: 1 / Mutation: R60E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.73 % / Mosaicity: 0.09 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.5 uL ~12 mg/mL R60E-CDO + 0.5 uL reservoir (26% w/v PEG4000, 200 mM ammonium acetate, 100 mM sodium citrate), cryo-protection: 20% w/v ethylene glycol + 80% reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9534 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 20, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9534 Å / Relative weight: 1
ReflectionResolution: 1.61→41.8 Å / Num. obs: 27402 / % possible obs: 99.9 % / Redundancy: 27.6 % / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.025 / Rrim(I) all: 0.132 / Net I/σ(I): 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.61-1.6417.61.5152300813080.6560.3591.559298.2
8.81-41.820.40.037461922610.0080.03866.899.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.07 Å41.8 Å
Translation5.07 Å41.8 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.15rc1-3423refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KWJ

4kwj


Resolution: 1.61→41.798 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 19.76
RfactorNum. reflection% reflection
Rfree0.2182 2397 4.74 %
Rwork0.1832 --
obs0.1848 27329 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.54 Å2 / Biso mean: 21.7586 Å2 / Biso min: 8.19 Å2
Refinement stepCycle: final / Resolution: 1.61→41.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 1 131 1642
Biso mean--13.32 31.41 -
Num. residues----186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.61-1.64170.29981560.2812277998
1.6417-1.67740.35991210.2572854100
1.6774-1.71640.29071710.23612804100
1.7164-1.75940.20821330.21462837100
1.7594-1.80690.22121420.20282861100
1.8069-1.86010.22711270.18662852100
1.8601-1.92010.23611500.1882850100
1.9201-1.98880.20891550.18852813100
1.9888-2.06840.15691240.16952839100
2.0684-2.16250.18011430.17032816100
2.1625-2.27650.22531250.16832867100
2.2765-2.41910.1951290.17512837100
2.4191-2.60590.21921450.1882860100
2.6059-2.86810.23211360.17442843100
2.8681-3.2830.24991400.17492825100
3.283-4.13560.19421540.17282827100
4.1356-41.7980.21051460.17672837100

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