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- PDB-6fx9: The X-ray structure of the ferritin nanocage containing Au and Pt... -

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Basic information

Entry
Database: PDB / ID: 6fx9
TitleThe X-ray structure of the ferritin nanocage containing Au and Pt, obtained upon encapsulation of a single heterobimetallic compound within the protein cage (synchrtron data)
ComponentsFerritin light chain
KeywordsMETAL TRANSPORT
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / cytoplasmic vesicle / intracellular iron ion homeostasis / iron ion binding / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMerlino, A. / Ferraro, G.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Caged noble metals: Encapsulation of a cytotoxic platinum(II)-gold(I) compound within the ferritin nanocage.
Authors: Ferraro, G. / Petruk, G. / Maiore, L. / Pane, F. / Amoresano, A. / Cinellu, M.A. / Monti, D.M. / Merlino, A.
History
DepositionMar 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,71319
Polymers19,8721
Non-polymers1,84018
Water4,143230
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)521,108456
Polymers476,93824
Non-polymers44,170432
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_995-y+4,-x+4,-z1
crystal symmetry operation11_577y,-z+2,-x+21
crystal symmetry operation7_793-z+2,-x+4,y-21
crystal symmetry operation19_977-x+4,-z+2,-y+21
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation10_977-y+4,z+2,-x+21
crystal symmetry operation8_757-z+2,x,-y+21
crystal symmetry operation18_973-x+4,z+2,y-21
crystal symmetry operation23_753-z+2,y,x-21
crystal symmetry operation2_995-x+4,-y+4,z1
crystal symmetry operation6_797z+2,-x+4,-y+21
crystal symmetry operation20_573x,-z+2,y-21
crystal symmetry operation12_973-y+4,-z+2,x-21
crystal symmetry operation15_595y,-x+4,z1
crystal symmetry operation17_577x,z+2,-y+21
crystal symmetry operation5_753z+2,x,y-21
crystal symmetry operation9_573y,z+2,x-21
crystal symmetry operation16_955-y+4,x,z1
crystal symmetry operation22_793z+2,-y+4,x-21
crystal symmetry operation24_797-z+2,-y+4,-x+21
crystal symmetry operation3_955-x+4,y,-z1
crystal symmetry operation4_595x,-y+4,-z1
crystal symmetry operation21_757z+2,y,-x+21
Unit cell
Length a, b, c (Å)181.680, 181.680, 181.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-204-

CD

21A-207-

CD

31A-217-

CD

41A-448-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791

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Non-polymers , 6 types, 248 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.6 M ammonium sulfate 0.1 M Tris HCl pH 7.4 60 mM cadmium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→104.9 Å / Num. obs: 41265 / % possible obs: 99.8 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.039 / Net I/σ(I): 12.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.592 / Rpim(I) all: 0.279 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ERK

5erk


Resolution: 1.5→104.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.134 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18282 2004 4.9 %RANDOM
Rwork0.15194 ---
obs0.15348 39257 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.241 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.5→104.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 27 230 1636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0191526
X-RAY DIFFRACTIONr_bond_other_d0.0020.021451
X-RAY DIFFRACTIONr_angle_refined_deg2.1991.9652039
X-RAY DIFFRACTIONr_angle_other_deg1.0883.0013308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4595189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90524.21783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71715277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1731513
X-RAY DIFFRACTIONr_chiral_restr0.1360.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021762
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02373
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9561.39726
X-RAY DIFFRACTIONr_mcbond_other1.9031.384725
X-RAY DIFFRACTIONr_mcangle_it2.8332.066919
X-RAY DIFFRACTIONr_mcangle_other2.8332.071920
X-RAY DIFFRACTIONr_scbond_it3.9971.847796
X-RAY DIFFRACTIONr_scbond_other3.9951.848797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6992.5531117
X-RAY DIFFRACTIONr_long_range_B_refined7.52712.8851835
X-RAY DIFFRACTIONr_long_range_B_other7.04312.091772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 159 -
Rwork0.251 2817 -
obs--99.03 %

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