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- PDB-9dy4: Crystal structure of iron-bound human ADO C18S/C239S variant soak... -

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Basic information

Entry
Database: PDB / ID: 9dy4
TitleCrystal structure of iron-bound human ADO C18S/C239S variant soaked in hydralazine at 2.39 Angstrom resolution
Components2-aminoethanethiol dioxygenase
KeywordsOXIDOREDUCTASE / cysteamine dioxygenase / cobalt-bound human ADO
Function / homology
Function and homology information


cysteamine dioxygenase / cysteamine dioxygenase activity / Degradation of cysteine and homocysteine / cellular response to hypoxia / iron ion binding / mitochondrion / cytosol
Similarity search - Function
Cysteine oxygenase/2-aminoethanethiol dioxygenase / PCO_ADO / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / 1-hydrazinophthalazine / 2-aminoethanethiol dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLiu, A. / Li, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2204225 United States
CitationJournal: To Be Published
Title: Hydralazine inhibits cysteamine dioxygenase to treat preeclampsia and senesce glioblastoma
Authors: Liu, A. / Li, J. / Ran, D. / Inchul, S.
History
DepositionOct 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-aminoethanethiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5085
Polymers30,1081
Non-polymers4004
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.203, 95.175, 117.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 2-aminoethanethiol dioxygenase / Cysteamine dioxygenase


Mass: 30108.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADO / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SZ5
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HLZ / 1-hydrazinophthalazine / Hydralazine / phthalazin-1-ylhydrazine


Mass: 160.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M (NH4)2SO4, 0.1 M Bis-Tris pH 5.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 12657 / % possible obs: 98.2 % / Redundancy: 7.6 % / CC1/2: 0.951 / CC star: 0.987 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.069 / Rrim(I) all: 0.194 / Χ2: 0.981 / Net I/σ(I): 4.1 / Num. measured all: 95946
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.39-2.435.40.8055860.8760.9660.3510.8840.55994.1
2.43-2.485.50.6846090.910.9760.2950.750.62697
2.48-2.525.60.7286040.8270.9510.3130.7980.60693.6
2.52-2.575.90.5415880.960.990.2210.5870.64493.6
2.57-2.635.90.5646120.920.9790.2340.6140.65495.3
2.63-2.696.40.5926000.8770.9670.2440.6430.97295.5
2.69-2.766.30.5516280.9210.9790.2250.5970.68997.5
2.76-2.836.40.4346200.9710.9930.1790.4710.72998.7
2.83-2.927.80.4116370.9730.9930.1550.440.70599.4
2.92-3.018.30.3676160.9730.9930.1370.3920.76399.5
3.01-3.128.60.356510.9780.9940.1280.3730.76799.8
3.12-3.249.10.3166460.9430.9850.1150.3370.83399.8
3.24-3.398.90.2496310.9830.9960.090.2650.896100
3.39-3.578.70.2326400.980.9950.0880.2491.166100
3.57-3.798.30.1956460.970.9920.0760.211.24699.8
3.79-4.099.20.1936480.9850.9960.070.2061.39599.8
4.09-4.59.10.166530.9830.9960.060.1711.24100
4.5-5.158.70.1576560.9770.9940.0580.1681.29499.8
5.15-6.488.30.156680.980.9950.0570.1611.3299.7
6.48-508.10.1327180.9880.9970.050.1421.4599.9

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
DENZO1.21data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→48.39 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 44.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.308 1235 9.88 %
Rwork0.253 --
obs0.258 12504 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 25 19 1870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081901
X-RAY DIFFRACTIONf_angle_d1.0652583
X-RAY DIFFRACTIONf_dihedral_angle_d20.459727
X-RAY DIFFRACTIONf_chiral_restr0.048272
X-RAY DIFFRACTIONf_plane_restr0.01343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.490.52941260.51061180X-RAY DIFFRACTION93
2.49-2.60.47821350.42671175X-RAY DIFFRACTION93
2.6-2.740.45481250.39351213X-RAY DIFFRACTION95
2.74-2.910.44021430.37831229X-RAY DIFFRACTION96
2.91-3.130.41481340.3021243X-RAY DIFFRACTION98
3.13-3.450.33511400.24941284X-RAY DIFFRACTION99
3.45-3.950.29841420.22051281X-RAY DIFFRACTION99
3.95-4.970.24821410.19311292X-RAY DIFFRACTION100
4.97-48.390.24431490.21741372X-RAY DIFFRACTION100

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