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- PDB-7zc3: Crystal structure of human copper chaperone Atox1 bound to zinc i... -

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Basic information

Entry
Database: PDB / ID: 7zc3
TitleCrystal structure of human copper chaperone Atox1 bound to zinc ion by CxxC motif
ComponentsCopper transport protein ATOX1
KeywordsCHAPERONE / Copper Transport Protein / Metallochaperone / Atox1 Protein / Metal Ions / Zinc
Function / homology
Function and homology information


metallochaperone activity / Ion influx/efflux at host-pathogen interface / copper-dependent protein binding / copper chaperone activity / copper ion transport / Detoxification of Reactive Oxygen Species / cuprous ion binding / intracellular copper ion homeostasis / response to oxidative stress / copper ion binding / cytosol
Similarity search - Function
: / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA
Similarity search - Domain/homology
Copper transport protein ATOX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMangini, V. / Belviso, B.D. / Arnesano, F. / Caliandro, R.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education2017WBZFHL_006 Italy
CitationJournal: Biomolecules / Year: 2022
Title: Crystal Structure of the Human Copper Chaperone ATOX1 Bound to Zinc Ion.
Authors: Mangini, V. / Belviso, B.D. / Nardella, M.I. / Natile, G. / Arnesano, F. / Caliandro, R.
History
DepositionMar 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 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: Copper transport protein ATOX1
B: Copper transport protein ATOX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4679
Polymers14,8252
Non-polymers6427
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-100 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.226, 78.226, 54.637
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Copper transport protein ATOX1 / Metal transport protein ATX1


Mass: 7412.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATOX1, HAH1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: O00244
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.26 Å3/Da / Density % sol: 62.21 % / Description: Needle-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Drop:12.5mg/ml Atox1 + 1.62mM ZnSO4 in 25mM Sodium Phosphate buffer pH 7.0, 2mM DTT; Reservoir: 1.9M Li2SO4, 100mM MES pH 6.0, 2.5% glycerol; VAPOR DIFFUSION, SITTING DROP, temperature 293K.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.28 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 12, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.9→39.04 Å / Num. obs: 23876 / % possible obs: 94.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 27.48 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 887 / CC1/2: 0.765 / % possible all: 92

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
Sir2014phasing
PHENIXmodel building
PHENIX1.19.2_4158refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qot

4qot


Resolution: 1.9→25.61 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1859 1214 5.08 %
Rwork0.165 22662 -
obs0.1662 23876 81.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.78 Å2 / Biso mean: 32.4581 Å2 / Biso min: 15.8 Å2
Refinement stepCycle: final / Resolution: 1.9→25.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 31 141 1184
Biso mean--52.33 43.04 -
Num. residues----134
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.980.31691530.2352487264082
1.98-2.070.28011720.20592566273884
2.07-2.180.21651550.17622572272784
2.18-2.320.20471080.20142555266382
2.32-2.490.21881130.19022668278186
2.49-2.740.21371230.19242700282387
2.75-3.140.20541150.20012531264681
3.14-3.950.16411330.13712360249377
3.96-25.610.13771420.12152223236573

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