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

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Basic information

Entry
Database: PDB / ID: 9dxv
TitleCrystal structure of cobalt-incorporated human 2-aminoethanethiol (aka cysteamine) dioxygenase (ADO) variant C18S/C239S in complex with CP6-L8K-Ser
Components
  • 2-aminoethanethiol dioxygenase
  • CP6-L8K-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
: / THIOCYANATE ION / 2-aminoethanethiol dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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-L8K-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,77216
Polymers31,7092
Non-polymers1,06314
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-44 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.939, 71.588, 108.526
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-L8K-Ser


Mass: 1867.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 235 molecules

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


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium nitrate, 20% w/v PEG3350, 0.1 M Bis-Tris propane, pH 6.5

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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: Aug 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→43.24 Å / Num. obs: 37903 / % possible obs: 99.3 % / Redundancy: 13.2 % / Biso Wilson estimate: 25.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 19
Reflection shellResolution: 1.6→1.62 Å / Num. unique obs: 1616 / CC1/2: 0.666

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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: 1.6→43.24 Å / SU ML: 0.1537 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1916 1896 5.02 %
Rwork0.1706 35905 -
obs0.1716 37801 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.79 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 62 221 2222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752144
X-RAY DIFFRACTIONf_angle_d1.04022918
X-RAY DIFFRACTIONf_chiral_restr0.0638312
X-RAY DIFFRACTIONf_plane_restr0.0117378
X-RAY DIFFRACTIONf_dihedral_angle_d11.0612316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28371270.24912287X-RAY DIFFRACTION89.11
1.64-1.680.21141320.20492510X-RAY DIFFRACTION99.89
1.68-1.730.20421380.19532557X-RAY DIFFRACTION99.96
1.73-1.790.24771470.20652536X-RAY DIFFRACTION100
1.79-1.850.2421260.20132532X-RAY DIFFRACTION100
1.85-1.920.21141230.17492560X-RAY DIFFRACTION100
1.92-2.010.17411360.16182591X-RAY DIFFRACTION100
2.01-2.120.18281490.16282556X-RAY DIFFRACTION99.96
2.12-2.250.19151250.17972584X-RAY DIFFRACTION100
2.25-2.420.22491230.1782567X-RAY DIFFRACTION99.96
2.42-2.670.23441530.18742577X-RAY DIFFRACTION100
2.67-3.050.19771350.18032610X-RAY DIFFRACTION100
3.05-3.850.17851270.15792656X-RAY DIFFRACTION99.93
3.85-43.240.16671550.15672782X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3861759861360.07743014045930.1820779470060.2805660333770.04326593750910.2114620520480.0784494274401-0.4975063983560.2348065544760.129396568199-0.0184184602206-0.261533971818-0.2574006602310.5013483622930.002023030490230.260661998813-0.0625740643764-0.01237062337410.330867333416-0.0495065956720.32428349521-1.97919254634-9.8319911238329.5543383533
21.45784244591-0.238346688218-0.0465864953420.8588354351080.04468370912671.351510545990.02140971241960.0222880589175-0.09063970356960.0162555710841-0.000246429687930.00710596827315-0.0834424035693-0.0333885541044-3.69391522152E-50.182441185384-0.006869961502250.006155716417960.160543762698-0.002517874497510.199745913388-16.2723034852-19.868668150420.7869530456
30.184470074291-0.2172264126320.05693810973320.221242799682-0.005145465643260.3187525164720.100298409679-0.192682586982-0.0426037989914-0.1711778035180.02019215838810.0256690293340.0920190536940.3254083015421.21233315913E-50.360319792454-0.0192812004766-0.01865577157430.4018748594670.005956153266440.215873558489-14.1840365762-19.2716721579-10.7940413598
41.211802475990.091390819172-0.09139662013980.5653883239170.04164889138372.219614046430.01465344082740.217963293432-0.0387033497893-0.06846541151490.00267157407386-0.00692399751086-0.118094126624-0.02290409503481.46962178283E-50.1980989878570.008113361252430.01305713053990.193490235914-0.009839580467350.208774534259-12.8913121306-17.664731720612.5499309473
50.0958587486615-0.0111238981738-0.05881632629460.05345835332360.009043434586180.026425003018-0.0713051950.05813724760920.0928946331163-0.1002273739970.05498647482960.313224915034-0.200802858919-0.21462445912-0.000210842227810.3613417395150.0421198914673-0.003496278167510.348968573998-0.007776933114320.382031645835-23.7863394269-10.202081010714.8494247999
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 60 )AA5 - 601 - 35
22chain 'A' and (resid 61 through 135 )AA61 - 13536 - 110
33chain 'A' and (resid 136 through 165 )AA136 - 165111 - 134
44chain 'A' and (resid 166 through 270 )AA166 - 270135 - 229
55chain 'B' and (resid 2 through 15 )BC - F2 - 153

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