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- PDB-3iwx: Crystal structure of cisplatin bound to a human copper chaperone ... -

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Basic information

Entry
Database: PDB / ID: 3iwx
TitleCrystal structure of cisplatin bound to a human copper chaperone (dimer)
ComponentsCopper transport protein ATOX1
KeywordsMETAL TRANSPORT / beta-alpha-beta-beta-alpha-beta / transport protein / cisplatin / platinum / Chaperone / Copper transport / Ion transport / Metal-binding / Transport
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
Cisplatin / Copper transport protein ATOX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsBoal, A.K. / Rosenzweig, A.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Crystal structures of cisplatin bound to a human copper chaperone.
Authors: Boal, A.K. / Rosenzweig, A.C.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)15,4146
Polymers14,8252
Non-polymers5884
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-58 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.289, 78.289, 54.335
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 / 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 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00244
#2: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 62.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5 M lithium sulfate, 0.1M MES, 50 mM NaCl, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 10562

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→28.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.17 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 504 4.8 %RANDOM
Rwork0.186 ---
obs0.188 10536 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.23 Å2 / Biso mean: 24.288 Å2 / Biso min: 13.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.14→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 18 105 1134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221034
X-RAY DIFFRACTIONr_angle_refined_deg1.0922.011389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6065132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66225.88234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56715201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.208152
X-RAY DIFFRACTIONr_chiral_restr0.0720.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02708
X-RAY DIFFRACTIONr_mcbond_it0.4461.5661
X-RAY DIFFRACTIONr_mcangle_it0.89821062
X-RAY DIFFRACTIONr_scbond_it1.6243373
X-RAY DIFFRACTIONr_scangle_it2.5974.5327
LS refinement shellResolution: 2.142→2.198 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 37 -
Rwork0.206 727 -
all-764 -
obs--100 %
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)
13.5144-0.53510.36094.6825-0.30494.1899-0.1489-0.02960.11030.01410.0555-0.0473-0.1814-0.07650.09340.03580.0113-0.00590.00670.01270.09721.8823-1.98054.503
22.12080.35671.31233.16261.09114.4005-0.03430.05310.0626-0.00430.1083-0.0421-0.02650.1345-0.0740.08520.00050.03250.04690.01280.030939.3026-16.54923.1873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 68
2X-RAY DIFFRACTION1A69 - 71
3X-RAY DIFFRACTION1A72 - 113
4X-RAY DIFFRACTION2B2 - 68
5X-RAY DIFFRACTION2B70 - 71
6X-RAY DIFFRACTION2B72 - 134

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