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- PDB-4qot: Crystal structure of human copper chaperone bound to the platinum ion -

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Basic information

Entry
Database: PDB / ID: 4qot
TitleCrystal structure of human copper chaperone bound to the platinum ion
ComponentsCopper transport protein ATOX1
KeywordsCHAPERONE / Metal-binding / Metal transport / platinum / oxaliplatin
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 / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Copper transport protein ATOX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBelviso, B.D. / Galliani, A. / Caliandro, R. / Arnesano, F. / Natile, G.
CitationJournal: Inorg.Chem. / Year: 2016
Title: Oxaliplatin Binding to Human Copper Chaperone Atox1 and Protein Dimerization
Authors: Belviso, B.D. / Galliani, A. / Lasorsa, A. / Mirabelli, V. / Caliandro, R. / Arnesano, F. / Natile, G.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)15,6969
Polymers14,8252
Non-polymers8707
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-112 kcal/mol
Surface area7110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.055, 78.055, 54.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Copper transport protein ATOX1 / Copper chaperone / 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 (E. coli) / References: UniProt: O00244, EC: 3.6.3.54
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12mg/mlATOX-Pt(DACH)(H2O)(SO4), 65% sat Li2SO4, 100mM MES, 60mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.071564 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 21, 2014
RadiationMonochromator: Si(311) high resolution monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071564 Å / Relative weight: 1
ReflectionResolution: 1.5→60 Å / Num. obs: 9697 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.3 Å / % possible all: 97

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Processing

Software
NameVersionClassification
MxCuBEdata collection
ILMILIONEmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
ILMILIONEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FEE

1fee


Resolution: 2.2→42.49 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 465 4.82 %
Rwork0.188 --
obs0.19 9647 99.3 %
all-9697 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 27 48 1087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081077
X-RAY DIFFRACTIONf_angle_d1.0631444
X-RAY DIFFRACTIONf_dihedral_angle_d13.544400
X-RAY DIFFRACTIONf_chiral_restr0.076167
X-RAY DIFFRACTIONf_plane_restr0.008176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2012-2.51970.2871560.24293026X-RAY DIFFRACTION99
2.5197-3.17450.27281690.22363050X-RAY DIFFRACTION100
3.1745-42.49610.2061400.16043106X-RAY DIFFRACTION99
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)
10.02830.16590.21180.96811.24531.61180.10330.1397-0.0239-0.1434-0.09120.05250.1025-0.0179-0.00670.3115-0.0461-0.03880.23180.0630.216224.2328151.454-34.9802
21.46350.0344-0.33663.43211.52972.45230.0116-0.08790.16490.00720.1063-0.0913-0.26680.2624-0.12360.4844-0.1155-0.18490.286-0.11650.392743.2217159.6953-36.0526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 15:15) or (chain A and resseq 12:12) or (chain B and resseq 15:15) or (chain B and resseq 12:12) or (chain A and resseq 101:101)
2X-RAY DIFFRACTION2(chain B and resseq 5:5 and altloc 'B') or (chain B and resseq 101:101) or (chain B and resseq 104:104) or (chain B and resseq 41:41 and altloc 'A') or (chain B and resseq 3:3 and altloc 'A')

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