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- PDB-9dma: Crystal structure of cobalt-bound human ADO C18S/C239S variant in... -

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Basic information

Entry
Database: PDB / ID: 9dma
TitleCrystal structure of cobalt-bound human ADO C18S/C239S variant in complex with hydralazine at 1.89 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: 1.89 Å
AuthorsLiu, A. / Li, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2204225 United States
CitationJournal: Sci Adv / Year: 2025
Title: Hydralazine inhibits cysteamine dioxygenase to treat preeclampsia and senesce glioblastoma.
Authors: Shishikura, K. / Li, J. / Chen, Y. / McKnight, N.R. / Keeley, T.P. / Bustin, K.A. / Barr, E.W. / Chilkamari, S.R. / Ayub, M. / Kim, S.W. / Lin, Z. / Hu, R.M. / Hicks, K. / Wang, X. / ...Authors: Shishikura, K. / Li, J. / Chen, Y. / McKnight, N.R. / Keeley, T.P. / Bustin, K.A. / Barr, E.W. / Chilkamari, S.R. / Ayub, M. / Kim, S.W. / Lin, Z. / Hu, R.M. / Hicks, K. / Wang, X. / O'Rourke, D.M. / Martin Bollinger Jr., J. / Binder, Z.A. / Parsons, W.H. / Martemyanov, K.A. / Liu, A. / Matthews, M.L.
History
DepositionSep 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)30,8608
Polymers30,1081
Non-polymers7527
Water1,78399
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)56.343, 95.052, 117.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 106 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HLZ / 1-hydrazinophthalazine / Hydralazine / phthalazin-1-ylhydrazine


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.81 %
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: 0.97145 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97145 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 24951 / % possible obs: 96.8 % / Redundancy: 8.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.035 / Rrim(I) all: 0.108 / Χ2: 0.938 / Net I/σ(I): 4.6 / Num. measured all: 206106
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.89-1.926.40.77911570.5170.8260.30.8440.81992.3
1.92-1.966.90.62811480.8350.9540.2320.6750.79590.5
1.96-26.80.612010.8290.9520.2260.6460.80994.3
2-2.0470.4611570.8870.970.1720.4940.81791.1
2.04-2.087.40.42411730.8780.9670.1570.4560.87392.4
2.08-2.1380.35812060.9620.990.1240.3810.84494.6
2.13-2.188.20.3612180.950.9870.1270.3840.84996.1
2.18-2.248.30.30512480.960.990.1070.3250.84996.8
2.24-2.318.30.28412530.9630.9910.1010.3030.91597.7
2.31-2.388.60.24812390.9830.9960.0860.2630.88998.1
2.38-2.478.30.21212580.9880.9970.0750.2250.92798.7
2.47-2.578.90.19512600.990.9980.0660.2060.90698.1
2.57-2.689.20.17312790.9930.9980.0570.1830.972100
2.68-2.829.10.1512870.9940.9990.050.1580.98799.5
2.82-39.10.1212800.9960.9990.040.1271.03899.9
3-3.238.50.10812850.9950.9990.0370.1141.11698.3
3.23-3.569.20.08812960.9970.9990.0290.0931.13999.5
3.56-4.079.10.07813080.9980.9990.0260.0821.131100
4.07-5.138.50.07113090.9970.9990.0240.0751.0498.4
5.13-508.60.05513890.99810.0190.0590.80799

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Processing

Software
NameVersionClassification
DENZO1.21data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.21refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→48.47 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2558 1995 8.06 %
Rwork0.2126 --
obs0.2161 24745 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 48 100 2041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062006
X-RAY DIFFRACTIONf_angle_d0.8672728
X-RAY DIFFRACTIONf_dihedral_angle_d17.132769
X-RAY DIFFRACTIONf_chiral_restr0.052284
X-RAY DIFFRACTIONf_plane_restr0.009362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.930.42761360.38261424X-RAY DIFFRACTION86
1.93-1.980.36271240.35251538X-RAY DIFFRACTION91
1.98-2.040.31961400.30291481X-RAY DIFFRACTION90
2.04-2.110.33721300.27171585X-RAY DIFFRACTION93
2.11-2.180.25911320.26741587X-RAY DIFFRACTION95
2.18-2.270.29981430.2481629X-RAY DIFFRACTION96
2.27-2.370.29811410.22581633X-RAY DIFFRACTION98
2.37-2.50.29331370.22711661X-RAY DIFFRACTION97
2.5-2.660.28291520.22151653X-RAY DIFFRACTION99
2.66-2.860.27751450.23391683X-RAY DIFFRACTION99
2.86-3.150.28251560.21491691X-RAY DIFFRACTION99
3.15-3.60.27881530.20611675X-RAY DIFFRACTION99
3.61-4.540.20421490.17521727X-RAY DIFFRACTION100
4.54-48.470.20321570.17591783X-RAY DIFFRACTION98

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