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- PDB-9ndu: Crystal Structure of Ferric Human ADO C18S/C239S Variant in Compl... -

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Basic information

Entry
Database: PDB / ID: 9ndu
TitleCrystal Structure of Ferric Human ADO C18S/C239S Variant in Complex with Hydralazine at 1.98 Angstrom Resolution
Components2-aminoethanethiol dioxygenase
KeywordsOXIDOREDUCTASE / cysteamine dioxygenase
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: 1.98 Å
AuthorsLiu, A. / Li, J. / Duan, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF CHE-2204225 United States
CitationJournal: To Be Published
Title: Crystal Structure of Ferric Human ADO C18S/C239S Variant in Complex with Hydralazine at 1.98 Angstrom Resolution
Authors: Liu, A. / Li, J. / Duan, R.
History
DepositionFeb 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-aminoethanethiol dioxygenase
B: 2-aminoethanethiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,64212
Polymers59,5092
Non-polymers1,13310
Water2,612145
1
A: 2-aminoethanethiol dioxygenase
hetero molecules

B: 2-aminoethanethiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,64212
Polymers59,5092
Non-polymers1,13310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area3110 Å2
ΔGint-90 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.607, 87.468, 118.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2-aminoethanethiol dioxygenase / Cysteamine dioxygenase


Mass: 29754.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADO, C10orf22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SZ5, cysteamine dioxygenase

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Non-polymers , 5 types, 155 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HLZ / 1-hydrazinophthalazine / Hydralazine / phthalazin-1-ylhydrazine


Mass: 160.176 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H8N4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
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: Nov 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 40543 / % possible obs: 99 % / Redundancy: 7.8 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.041 / Rrim(I) all: 0.118 / Χ2: 0.981 / Net I/σ(I): 6.1 / Num. measured all: 315464
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.98-2.016.20.99819170.8080.9450.3931.0780.57695.3
2.01-2.056.50.82919510.8720.9650.3220.8930.59597.1
2.05-2.096.80.78119710.8160.9480.3050.8420.80298.6
2.09-2.137.20.71520170.9270.9810.2720.7671.14198.6
2.13-2.187.50.64319850.9280.9810.2420.6890.6199.3
2.18-2.237.90.58420140.9490.9870.2170.6250.63299.8
2.23-2.2980.57320110.6290.8790.2240.6171.12899.8
2.29-2.358.10.48720040.9580.9890.180.520.67399.3
2.35-2.4280.39320680.980.9950.1470.420.71599.8
2.42-2.497.50.33619840.9760.9940.1310.3620.73799.3
2.49-2.5880.28920040.9840.9960.1080.3090.7698.7
2.58-2.698.60.25120110.990.9980.090.2670.86599.4
2.69-2.818.60.19620420.9940.9990.070.2080.8499.6
2.81-2.968.40.14620400.9950.9990.0530.1550.95999.7
2.96-3.148.30.11820470.9960.9990.0430.1261.0499.9
3.14-3.3980.09620250.9970.9990.0360.1031.22599.5
3.39-3.737.40.07220560.9970.9990.0280.0781.38298.5
3.73-4.268.60.06120820.99810.0220.0651.447100
4.26-5.378.30.05421070.99810.020.0581.34799.9
5.37-507.50.05822070.9980.9990.0220.0621.80398.4

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Processing

Software
NameVersionClassification
DENZO1.21data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.21_5207-000refinement
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→43.62 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 1996 4.95 %
Rwork0.2175 --
obs0.2198 40329 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 71 145 3916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073890
X-RAY DIFFRACTIONf_angle_d0.975303
X-RAY DIFFRACTIONf_dihedral_angle_d17.2391480
X-RAY DIFFRACTIONf_chiral_restr0.051556
X-RAY DIFFRACTIONf_plane_restr0.009706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.35311330.32662538X-RAY DIFFRACTION93
2.03-2.090.33611370.30582674X-RAY DIFFRACTION98
2.09-2.150.36421410.26852696X-RAY DIFFRACTION99
2.15-2.220.31391420.25572730X-RAY DIFFRACTION99
2.22-2.30.31151430.25022737X-RAY DIFFRACTION99
2.3-2.390.28151400.24772685X-RAY DIFFRACTION99
2.39-2.50.31641430.2372739X-RAY DIFFRACTION99
2.5-2.630.28481420.22522724X-RAY DIFFRACTION98
2.63-2.790.3051420.23132740X-RAY DIFFRACTION99
2.79-3.010.26741430.21952749X-RAY DIFFRACTION99
3.01-3.310.2851450.21322779X-RAY DIFFRACTION100
3.31-3.790.23591440.19562770X-RAY DIFFRACTION98
3.79-4.770.20381470.17652835X-RAY DIFFRACTION100
4.77-43.620.24851540.21292937X-RAY DIFFRACTION99

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