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- PDB-8u9j: The crystal structure of iron-bound human ADO C18S C239S variant ... -

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Basic information

Entry
Database: PDB / ID: 8u9j
TitleThe crystal structure of iron-bound human ADO C18S C239S variant at 2.02 Angstrom
Components2-aminoethanethiol dioxygenase
KeywordsOXIDOREDUCTASE / cysteamine dioxygenase (EC 1.13.11.19) / iron-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
: / 2-aminoethanethiol dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsLiu, A. / Li, J. / Duan, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2204225 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Cobalt(II)-Substituted Cysteamine Dioxygenase Oxygenation Proceeds through a Cobalt(III)-Superoxo Complex.
Authors: Li, J. / Duan, R. / Liu, A.
History
DepositionSep 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)60,88810
Polymers60,2162
Non-polymers6728
Water5,062281
1
A: 2-aminoethanethiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5366
Polymers30,1081
Non-polymers4285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-aminoethanethiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3524
Polymers30,1081
Non-polymers2443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.941, 55.198, 97.322
Angle α, β, γ (deg.)90.00, 114.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-aminoethanethiol dioxygenase / Cysteamine dioxygenase


Mass: 30108.080 Da / Num. of mol.: 2 / Mutation: C18S, C239S
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-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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
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: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 27, 2022
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 36519 / % possible obs: 96.7 % / Redundancy: 4.3 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.11 / Rrim(I) all: 0.256 / Χ2: 1.027 / Net I/σ(I): 5.1 / Num. measured all: 157446
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.01-2.042.80.92315280.6630.8930.5571.0850.48482.2
2.04-2.083.20.88315890.6420.8840.4891.0160.50285.5
2.08-2.123.40.79716550.7790.9360.4130.9030.53988.5
2.12-2.173.60.80817570.7620.930.4170.9140.49691.9
2.17-2.213.80.7817350.7550.9270.3920.8780.53993.9
2.21-2.263.90.72817970.7240.9170.3660.8190.59195.5
2.26-2.3240.62118390.8990.9730.3070.6950.60697.5
2.32-2.384.30.58118400.8920.9710.2830.6490.60698.9
2.38-2.454.50.5318830.8870.970.2530.590.64599.8
2.45-2.534.60.48418710.9320.9820.2280.5360.673100
2.53-2.624.70.41418990.9390.9840.1940.4580.7599.9
2.62-2.734.70.37118740.9520.9870.1740.4110.794100
2.73-2.854.80.31518870.9610.990.1450.3480.94100
2.85-34.80.26618770.9610.990.1220.2941.118100
3-3.194.80.22918870.9720.9930.1050.2521.164100
3.19-3.444.80.20319100.970.9920.0930.2241.494100
3.44-3.784.80.1818890.9710.9930.0830.1991.719100
3.78-4.334.80.16419220.9730.9930.0760.1811.813100
4.33-5.454.70.14419100.9740.9930.0680.161.6799.9
5.45-504.60.14419700.9750.9940.0680.161.88399.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487-000refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→46.84 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 1990 5.48 %
Rwork0.2082 --
obs0.211 36311 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 36 281 4117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083956
X-RAY DIFFRACTIONf_angle_d15395
X-RAY DIFFRACTIONf_dihedral_angle_d6.823545
X-RAY DIFFRACTIONf_chiral_restr0.056572
X-RAY DIFFRACTIONf_plane_restr0.008725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.36341150.30431939X-RAY DIFFRACTION77
2.07-2.120.32991270.26232194X-RAY DIFFRACTION86
2.12-2.190.27561320.25632290X-RAY DIFFRACTION91
2.19-2.260.33191380.25662392X-RAY DIFFRACTION94
2.26-2.340.26571430.25272468X-RAY DIFFRACTION97
2.34-2.430.30061440.23632516X-RAY DIFFRACTION99
2.43-2.540.26511460.22632512X-RAY DIFFRACTION100
2.54-2.670.29891480.21632538X-RAY DIFFRACTION99
2.67-2.840.30351480.21932558X-RAY DIFFRACTION100
2.84-3.060.25231480.20692563X-RAY DIFFRACTION100
3.06-3.370.24411480.20372546X-RAY DIFFRACTION100
3.37-3.860.22741500.17792573X-RAY DIFFRACTION100
3.86-4.860.23041490.16882590X-RAY DIFFRACTION100
4.86-46.840.23661540.20342642X-RAY DIFFRACTION100

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