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

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Basic information

Entry
Database: PDB / ID: 9dxu
TitleCrystal structure of cobalt-incorporated human 2-aminoethanethiol (aka cysteamine) dioxygenase (ADO) variant C18S/C239S in complex with CP6
Components
  • 2-aminoethanethiol dioxygenase
  • CP6
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: 1.74 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,64517
Polymers31,6072
Non-polymers1,03815
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-41 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.111, 71.605, 108.872
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


Mass: 1765.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 259 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG3350, 0.2 M sodium thiocyanate

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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 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.74→43.34 Å / Num. obs: 29565 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 23.81 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.3
Reflection shellResolution: 1.74→1.78 Å / Num. unique obs: 1542 / CC1/2: 0.73

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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→43.34 Å / SU ML: 0.2198 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2147 1478 5.01 %
Rwork0.1749 28037 -
obs0.1768 29515 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.36 Å2
Refinement stepCycle: LAST / Resolution: 1.74→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 57 244 2232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722200
X-RAY DIFFRACTIONf_angle_d1.01272998
X-RAY DIFFRACTIONf_chiral_restr0.064314
X-RAY DIFFRACTIONf_plane_restr0.009393
X-RAY DIFFRACTIONf_dihedral_angle_d9.7987320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.80.32861230.28952481X-RAY DIFFRACTION98.64
1.8-1.870.29031250.24092478X-RAY DIFFRACTION100
1.87-1.940.26211240.2162527X-RAY DIFFRACTION100
1.94-2.030.25841710.19242482X-RAY DIFFRACTION100
2.03-2.140.24941250.18342538X-RAY DIFFRACTION100
2.14-2.270.21471450.19742515X-RAY DIFFRACTION100
2.27-2.440.21011200.18062547X-RAY DIFFRACTION100
2.44-2.690.24511300.19042553X-RAY DIFFRACTION100
2.69-3.080.21621380.17892577X-RAY DIFFRACTION100
3.08-3.880.20281500.15062572X-RAY DIFFRACTION100
3.88-43.340.16661270.14972767X-RAY DIFFRACTION99.93
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)
16.771488928530.4297695796570.6522226314694.57914836313-0.9145922894845.892871407070.125590646893-0.34801865814-0.399980188514-0.0217327429969-0.0626860454730.3036696403960.4664364887-0.556145697599-0.03845382335410.150815022566-0.03927480563420.04251315715360.2053084749190.04687436567970.197141534227-16.239124051-26.205725215628.5712041219
22.205792202390.265046289047-0.2392218410551.47588995154-0.09725207552692.374407815340.004486645027220.05640307229090.104403096007-0.005690829902140.03767277202050.0418467602147-0.0283422944436-0.0753704396141-0.03640770519670.1138000830950.003270872375110.006412549743750.07741293531470.009494288901180.117114345056-1.60848241392-15.770310881120.8126745947
35.89077369356-4.09145099031-3.893023904724.134745350960.0325974080768.093612749620.063510036332-0.2854417294360.156984720606-0.1521946754870.01612359377770.101372618862-0.047181682899-0.831891904397-0.02928423965580.327888793881-0.0706994531104-0.007256447108940.3465246199170.03186762555480.142244393532-5.11478188319-14.6584777253-10.9857477383
40.9239610168150.358194128226-0.563975059960.519161372437-0.6342376599633.75865483967-0.03342658222550.1886687286160.0637928873919-0.09314615436480.01282206536050.08086644560490.0302799892072-0.5138502470670.01433144113750.13171819760.00543283879465-0.01998264856330.1768842231480.014491792330.180717826238-7.72687026247-17.855338506110.7630871675
51.554682625930.06513738473230.2815765347341.031747819640.1527681603824.18178840229-0.01564477366730.3429454996060.110570109507-0.2217635888210.007987914180830.0562127976076-0.0472276268007-0.162109785665-0.01539389587060.149694521502-0.00398278120054-0.00897642359590.1879861890240.01822305803870.142575158889-1.45376053605-18.692579038111.0951597066
66.106385715512.68265863043-6.736018168113.63772091181-3.017095879299.82726225465-0.102433009241-0.157852144828-0.2466324237960.300773547597-0.12226422443-0.4136799075860.2519345435540.2106668327170.1814719413360.206972226363-0.000425388232719-0.02053068272320.174295614282-0.009758723283290.2482229900546.75468242782-26.005890792315.2457620396
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 60 )AA7 - 602 - 35
22chain 'A' and (resid 61 through 135 )AA61 - 13536 - 110
33chain 'A' and (resid 136 through 158 )AA136 - 158111 - 126
44chain 'A' and (resid 159 through 216 )AA159 - 216127 - 184
55chain 'A' and (resid 217 through 270 )AA217 - 270185 - 228
66chain 'B' and (resid 1 through 14 )BC1 - 142 - 15

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