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- PDB-9dxb: Crystal structure of cobalt-incorporated human 2-aminoethanethiol... -

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Basic information

Entry
Database: PDB / ID: 9dxb
TitleCrystal structure of cobalt-incorporated human 2-aminoethanethiol (aka cysteamine) dioxygenase (ADO) variant C18S/C239S in complex with CP6-L8d-Gly-Ser
Components
  • 2-aminoethanethiol dioxygenase
  • CP6-L8d-Gly-Ser
KeywordsOXIDOREDUCTASE / oxygen-sensor / thiol 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
: / 2-aminoethanethiol dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsJiramongkol, Y. / Patel, K. / White, M.D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008546 Australia
CitationJournal: Nat Commun / Year: 2025
Title: An mRNA-display derived cyclic peptide scaffold reveals the substrate binding interactions of an N-terminal cysteine oxidase.
Authors: Jiramongkol, Y. / Patel, K. / Johansen-Leete, J. / Maxwell, J.W.C. / Chang, Y. / Du, J.J. / Passioura, T. / Cook, K.M. / Payne, R.J. / White, M.D.
History
DepositionOct 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: 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: CP6-L8d-Gly-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,31410
Polymers31,7242
Non-polymers5908
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-38 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.015, 71.879, 108.894
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein 2-aminoethanethiol dioxygenase / Cysteamine dioxygenase


Mass: 29841.811 Da / Num. of mol.: 1
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
#2: Protein/peptide CP6-L8d-Gly-Ser


Mass: 1882.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 208 molecules

#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-Tris, pH 5.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.74→43.4 Å / Num. obs: 30023 / % possible obs: 99.8 % / Redundancy: 13 % / Biso Wilson estimate: 28.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.4
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1527 / CC1/2: 0.852 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→43.4 Å / SU ML: 0.2312 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2177 1500 5.01 %
Rwork0.1761 28467 -
obs0.1782 29967 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.04 Å2
Refinement stepCycle: LAST / Resolution: 1.74→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 33 200 2188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722144
X-RAY DIFFRACTIONf_angle_d1.0062932
X-RAY DIFFRACTIONf_chiral_restr0.0634316
X-RAY DIFFRACTIONf_plane_restr0.0097384
X-RAY DIFFRACTIONf_dihedral_angle_d7.2881314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.36041190.33722494X-RAY DIFFRACTION97.54
1.79-1.860.29581340.24282529X-RAY DIFFRACTION99.96
1.86-1.930.22241250.19062547X-RAY DIFFRACTION100
1.93-2.020.23911580.16762563X-RAY DIFFRACTION100
2.02-2.120.23521370.17842573X-RAY DIFFRACTION99.96
2.12-2.260.21621490.19662554X-RAY DIFFRACTION99.93
2.26-2.430.21281250.18452565X-RAY DIFFRACTION100
2.43-2.680.24411280.18982609X-RAY DIFFRACTION100
2.68-3.060.24651440.18462595X-RAY DIFFRACTION100
3.06-3.860.20551500.16332633X-RAY DIFFRACTION100
3.86-43.40.18521310.15652805X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 4.7812567863 Å / Origin y: 18.9750758387 Å / Origin z: 15.4176287003 Å
111213212223313233
T0.183250514862 Å2-0.00261569276708 Å20.00565779026378 Å2-0.162795908544 Å20.00485082705398 Å2--0.193746675745 Å2
L0.922000509094 °20.0250937654406 °2-0.0800957942568 °2-0.462821180327 °2-0.0486703488105 °2--1.13532353208 °2
S0.024585221683 Å °0.045276546434 Å °0.0271323681195 Å °-0.0531552173863 Å °0.0114034099662 Å °0.00620821166717 Å °-0.0274193410145 Å °0.0133231369352 Å °-3.1775716536E-6 Å °
Refinement TLS groupSelection details: all

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