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- PDB-7rei: The crystal structure of nickel bound human ADO C18S C239S variant -

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Basic information

Entry
Database: PDB / ID: 7rei
TitleThe crystal structure of nickel bound human ADO C18S C239S variant
Components2-aminoethanethiol dioxygenase
KeywordsOXIDOREDUCTASE / non-heme iron-dependent dioxygenase
Function / homology
Function and homology information


cysteamine dioxygenase / cysteamine dioxygenase activity / Degradation of cysteine and homocysteine / cellular response to hypoxia / iron ion binding / 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
NICKEL (II) ION / 2-aminoethanethiol dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsWang, Y. / Shin, I. / Li, J. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1808637 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Crystal structure of human cysteamine dioxygenase provides a structural rationale for its function as an oxygen sensor.
Authors: Wang, Y. / Shin, I. / Li, J. / Liu, A.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-aminoethanethiol dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4589
Polymers29,7551
Non-polymers7038
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.881, 95.764, 117.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein 2-aminoethanethiol dioxygenase / Cysteamine dioxygenase


Mass: 29754.732 Da / Num. of mol.: 1 / Mutation: C18S, C239S
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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M LiSO4, 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: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 29671 / % possible obs: 99.4 % / Redundancy: 12.7 % / Biso Wilson estimate: 25.69 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.032 / Rrim(I) all: 0.114 / Χ2: 1.091 / Net I/σ(I): 5.7 / Num. measured all: 377079
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.8110.21.00414290.790.3191.0560.67797.9
1.81-1.84110.82914520.8560.2560.8690.73199.2
1.84-1.8811.80.76414600.890.2290.7990.77999.7
1.88-1.9212.20.70514610.9180.2090.7360.77999.7
1.92-1.9612.70.61515180.9420.1790.6410.80499.4
1.96-212.80.50114180.9650.1450.5220.85999.4
2-2.05120.40914600.9650.1210.4270.93198.4
2.05-2.1113.40.36814940.9750.1050.3830.96899.6
2.11-2.1713.70.3214700.9780.0910.3331.01599.9
2.17-2.2413.60.2914510.9850.0820.3011.02199.9
2.24-2.3213.30.2414950.9850.0690.251.08599.9
2.32-2.42130.21414700.9870.0620.2231.11999.6
2.42-2.5312.20.17914650.9890.0530.1871.22998.6
2.53-2.6613.70.1614900.9930.0460.1671.331100
2.66-2.8313.50.13714950.9910.0390.1421.34199.9
2.83-3.0413.30.11415110.9930.0330.1181.544100
3.04-3.3512.60.09514810.9960.0270.0981.59899.3
3.35-3.8313.70.07915200.9930.0220.0831.58899.9
3.83-4.8312.60.06215230.9960.0180.0651.31499.1
4.83-5012.80.04516080.9990.0130.0470.80799

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: customized ensenble

Resolution: 1.78→47.62 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 1990 6.72 %
Rwork0.1801 27637 -
obs0.1821 29627 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.3 Å2 / Biso mean: 32.4678 Å2 / Biso min: 15.5 Å2
Refinement stepCycle: final / Resolution: 1.78→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 43 212 2176
Biso mean--41.71 39.46 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072039
X-RAY DIFFRACTIONf_angle_d0.9082773
X-RAY DIFFRACTIONf_dihedral_angle_d13.564803
X-RAY DIFFRACTIONf_chiral_restr0.056291
X-RAY DIFFRACTIONf_plane_restr0.008371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.830.33181330.29031838197193
1.83-1.880.2921410.24451930207199
1.88-1.930.25241380.214419502088100
1.93-20.23231430.20211976211999
2-2.070.2421400.18451946208699
2.07-2.150.23461400.194519502090100
2.15-2.250.22321420.193319692111100
2.25-2.370.22631450.183519932138100
2.37-2.510.21351440.18841976212099
2.51-2.710.22831450.192119752120100
2.71-2.980.21281470.183619922139100
2.98-3.410.17871440.180220102154100
3.41-4.30.17891420.148620252167100
4.3-47.620.19721460.16942107225399

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