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- PDB-5ix6: X-ray structure of Auoxo3-encapsulated horse spleen apoferritin -

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Basic information

Entry
Database: PDB / ID: 5ix6
TitleX-ray structure of Auoxo3-encapsulated horse spleen apoferritin
ComponentsFerritin light chain
KeywordsTRANSPORT PROTEIN / ferritin / nanocage / metallodrugs / gold compounds
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFerraro, G. / Pontillo, N. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Regione Autonoma della SardegnaL.R. 7/2007 bando 2013. Italy
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: Gold-based drug encapsulation within a ferritin nanocage: X-ray structure and biological evaluation as a potential anticancer agent of the Auoxo3-loaded protein.
Authors: Ferraro, G. / Monti, D.M. / Amoresano, A. / Pontillo, N. / Petruk, G. / Pane, F. / Cinellu, M.A. / Merlino, A.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related
Item: _pdbx_database_related.db_id / _pdbx_database_related.details
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_CC_half
Revision 1.4Jan 10, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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

Downloads & links

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,35918
Polymers19,8721
Non-polymers2,48717
Water4,612256
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)536,615432
Polymers476,93824
Non-polymers59,677408
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_995-x+4,-y+4,z1
crystal symmetry operation3_955-x+4,y,-z1
crystal symmetry operation4_595x,-y+4,-z1
crystal symmetry operation5_753z+2,x,y-21
crystal symmetry operation6_797z+2,-x+4,-y+21
crystal symmetry operation7_793-z+2,-x+4,y-21
crystal symmetry operation8_757-z+2,x,-y+21
crystal symmetry operation9_573y,z+2,x-21
crystal symmetry operation10_977-y+4,z+2,-x+21
crystal symmetry operation11_577y,-z+2,-x+21
crystal symmetry operation12_973-y+4,-z+2,x-21
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_995-y+4,-x+4,-z1
crystal symmetry operation15_595y,-x+4,z1
crystal symmetry operation16_955-y+4,x,z1
crystal symmetry operation17_577x,z+2,-y+21
crystal symmetry operation18_973-x+4,z+2,y-21
crystal symmetry operation19_977-x+4,-z+2,-y+21
crystal symmetry operation20_573x,-z+2,y-21
crystal symmetry operation21_757z+2,y,-x+21
crystal symmetry operation22_793z+2,-y+4,x-21
crystal symmetry operation23_753-z+2,y,x-21
crystal symmetry operation24_797-z+2,-y+4,-x+21
Unit cell
Length a, b, c (Å)180.645, 180.645, 180.645
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-210-

CD

21A-212-

CD

31A-214-

CD

41A-309-

HOH

51A-539-

HOH

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Components

#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) / Organ: spleen / References: UniProt: P02791
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Au
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Crystals of Auoxo3-encapsulated AFt with diamond-like morphology, suitable for X-ray diffraction data collection, were grown by hanging-drop vapor diffusion technique at 293 K mixing the ...Details: Crystals of Auoxo3-encapsulated AFt with diamond-like morphology, suitable for X-ray diffraction data collection, were grown by hanging-drop vapor diffusion technique at 293 K mixing the protein (5-10 mg x mL-1) with equal volumes of a reservoir solution consisting of 0.6-0.8 M (NH4)2SO4, 0.1 M Tris pH 7.4-7.7, 50-60 mM CdSO4.
PH range: 7.4-7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 17, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→104.3 Å / Num. obs: 20893 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.666 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.102 / Rrim(I) all: 0.243 / Net I/σ(I): 9.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.8 / CC1/2: 0.284 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ERK

5erk


Resolution: 1.85→104.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.458 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22596 1128 5.1 %RANDOM
Rwork0.18024 ---
obs0.18256 20893 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.717 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.85→104.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 21 256 1662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191545
X-RAY DIFFRACTIONr_bond_other_d0.0020.021479
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9662096
X-RAY DIFFRACTIONr_angle_other_deg0.93233402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4135198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71224.09683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32915289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6941514
X-RAY DIFFRACTIONr_chiral_restr0.1170.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021828
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02382
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_it1.971.667754
X-RAY DIFFRACTIONr_mcbond_other1.961.658753
X-RAY DIFFRACTIONr_mcangle_it3.1342.469960
X-RAY DIFFRACTIONr_mcangle_other3.1382.479961
X-RAY DIFFRACTIONr_scbond_it2.8211.97789
X-RAY DIFFRACTIONr_scbond_other2.8041.961786
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4032.8231127
X-RAY DIFFRACTIONr_long_range_B_refined7.91215.7422088
X-RAY DIFFRACTIONr_long_range_B_other7.10614.3661935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 80 -
Rwork0.384 1447 -
obs--95.86 %

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