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- PDB-8b7o: X-ray structure of Auranofin-human H-chain ferritin -

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Basic information

Entry
Database: PDB / ID: 8b7o
TitleX-ray structure of Auranofin-human H-chain ferritin
ComponentsFerritin heavy chain, N-terminally processed
KeywordsTRANSPORT PROTEIN / ferritin / gold / encapsulation / auranofin / anticancer
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / : / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsFerraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2022
Title: Evaluation of Auranofin Loading within Ferritin Nanocages.
Authors: Lucignano, R. / Pratesi, A. / Imbimbo, P. / Monti, D.M. / Picone, D. / Messori, L. / Ferraro, G. / Merlino, A.
History
DepositionSep 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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
AAA: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,62921
Polymers21,1821
Non-polymers1,44820
Water7,098394
1
AAA: Ferritin heavy chain, N-terminally processed
hetero molecules
x 24


  • defined by software
  • 543 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)543,104504
Polymers508,35624
Non-polymers34,748480
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
MethodPISA
Unit cell
Length a, b, c (Å)184.030, 184.030, 184.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11AAA-201-

CL

21AAA-205-

MG

31AAA-206-

MG

41AAA-338-

HOH

51AAA-519-

HOH

61AAA-619-

HOH

71AAA-635-

HOH

81AAA-641-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Ferritin heavy chain, N-terminally processed


Mass: 21181.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02794

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Non-polymers , 5 types, 414 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.07 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.0 M magnesium chloride 0.1 M Bicine buffer pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→46.05 Å / Num. obs: 90295 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.018 / Rrim(I) all: 0.157 / Net I/σ(I): 26.6
Reflection shellResolution: 1.17→1.19 Å / Redundancy: 15 % / Rmerge(I) obs: 1.8 / Num. unique obs: 4445 / CC1/2: 0.777 / Rpim(I) all: 0.378 / Rrim(I) all: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N27

5n27


Resolution: 1.17→46.05 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.45 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1665 4431 4.945 %
Rwork0.149 85177 -
all0.15 --
obs-89608 99.967 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.745 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.17→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 20 394 1837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131682
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171499
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1180.0123
X-RAY DIFFRACTIONr_angle_refined_deg2.1961.6392294
X-RAY DIFFRACTIONr_angle_other_deg1.6571.5913532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7495216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6324.286105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48415325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.496158
X-RAY DIFFRACTIONr_chiral_restr0.120.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021976
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02348
X-RAY DIFFRACTIONr_nbd_refined0.3150.2447
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21241
X-RAY DIFFRACTIONr_nbtor_refined0.190.2768
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.2569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.270.2243
X-RAY DIFFRACTIONr_metal_ion_refined0.0610.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2790.212
X-RAY DIFFRACTIONr_nbd_other0.210.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.350.256
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0270.22
X-RAY DIFFRACTIONr_mcbond_it1.3281.093800
X-RAY DIFFRACTIONr_mcbond_other1.3081.09798
X-RAY DIFFRACTIONr_mcangle_it2.0151.6391025
X-RAY DIFFRACTIONr_mcangle_other1.9991.6381025
X-RAY DIFFRACTIONr_scbond_it2.6131.349882
X-RAY DIFFRACTIONr_scbond_other2.6111.35883
X-RAY DIFFRACTIONr_scangle_it4.0171.9661277
X-RAY DIFFRACTIONr_scangle_other3.991.9551271
X-RAY DIFFRACTIONr_lrange_it6.81316.5732205
X-RAY DIFFRACTIONr_lrange_other5.73114.6032064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.20.2323350.2296198X-RAY DIFFRACTION99.9694
1.2-1.2330.2323130.2166036X-RAY DIFFRACTION99.9843
1.233-1.2690.2382930.2085901X-RAY DIFFRACTION99.9355
1.269-1.3080.2213140.1975700X-RAY DIFFRACTION100
1.308-1.3510.2032990.1865537X-RAY DIFFRACTION99.9829
1.398-1.4510.1872760.1655197X-RAY DIFFRACTION99.9817
1.451-1.510.1582490.1515003X-RAY DIFFRACTION99.9049
1.51-1.5780.1562540.1364791X-RAY DIFFRACTION99.9802
1.578-1.6550.1442260.1314627X-RAY DIFFRACTION99.9176
1.655-1.7440.142280.134404X-RAY DIFFRACTION99.9784
1.744-1.850.1582130.1324168X-RAY DIFFRACTION100
1.85-1.9770.1532270.1293914X-RAY DIFFRACTION99.9759
1.977-2.1360.1431750.1273687X-RAY DIFFRACTION100
2.136-2.340.1451700.1233390X-RAY DIFFRACTION100
2.34-2.6160.1531650.1283103X-RAY DIFFRACTION100
2.616-3.020.1611490.1372755X-RAY DIFFRACTION100
3.02-3.6980.1351200.1332358X-RAY DIFFRACTION100
3.698-5.2260.158880.1361890X-RAY DIFFRACTION100

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