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- PDB-8b7l: X-ray structure of Auranofin-horse spleen ferritin -

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Basic information

Entry
Database: PDB / ID: 8b7l
TitleX-ray structure of Auranofin-horse spleen ferritin
ComponentsFerritin light chain
KeywordsTRANSPORT PROTEIN / ferritin / gold / encapsulation / auranofin / anticancer
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 / 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 light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,28415
Polymers19,8721
Non-polymers1,41114
Water6,071337
1
AAA: Ferritin light chain
hetero molecules

AAA: Ferritin light chain
hetero molecules

AAA: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,85145
Polymers59,6173
Non-polymers4,23342
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_753z+2,x,y-21
crystal symmetry operation9_573y,z+2,x-21
Unit cell
Length a, b, c (Å)181.990, 181.990, 181.990
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-204-

CD

21AAA-205-

CD

31AAA-208-

CD

41AAA-214-

CL

51AAA-516-

HOH

61AAA-527-

HOH

71AAA-557-

HOH

81AAA-609-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#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 , 5 types, 351 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.8 M ammonium sulphate 0.1 M TrisHCl pH 7.4 60 mM cadmium sulphate

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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 6M / 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: 1.24→64.34 Å / Num. obs: 88885 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.014 / Net I/σ(I): 34.9
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 15 % / Rmerge(I) obs: 1.8 / Num. unique obs: 3593 / CC1/2: 0.772 / Rpim(I) all: 0.364 / % 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: 5ERK

5erk


Resolution: 1.24→64.34 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.5 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1798 4449 5.005 %
Rwork0.1582 84436 -
all0.159 --
obs-88885 98.147 %
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: 15.916 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.24→64.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 27 337 1734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171520
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1980.017
X-RAY DIFFRACTIONr_angle_refined_deg2.2431.6362258
X-RAY DIFFRACTIONr_angle_other_deg1.661.5833545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16421.81105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67115311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0221516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021984
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02380
X-RAY DIFFRACTIONr_nbd_refined0.2920.2443
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21295
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2785
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2710.2216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1450.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3410.231
X-RAY DIFFRACTIONr_nbd_other0.2460.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3250.266
X-RAY DIFFRACTIONr_mcbond_it1.8991.27806
X-RAY DIFFRACTIONr_mcbond_other1.8011.266805
X-RAY DIFFRACTIONr_mcangle_it2.371.8941044
X-RAY DIFFRACTIONr_mcangle_other2.3691.8981045
X-RAY DIFFRACTIONr_scbond_it3.1061.601843
X-RAY DIFFRACTIONr_scbond_other3.0951.602840
X-RAY DIFFRACTIONr_scangle_it4.6722.2821211
X-RAY DIFFRACTIONr_scangle_other4.6812.2791205
X-RAY DIFFRACTIONr_lrange_it7.88519.3492136
X-RAY DIFFRACTIONr_lrange_other7.27517.3142010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.251-1.2890.2633080.2395765X-RAY DIFFRACTION100
1.331-1.3780.2052670.1985467X-RAY DIFFRACTION100
1.378-1.430.1982510.1825287X-RAY DIFFRACTION100
1.488-1.5550.1712490.1464888X-RAY DIFFRACTION100
1.555-1.630.1512670.1334628X-RAY DIFFRACTION100
1.63-1.7190.1432340.1264440X-RAY DIFFRACTION100
1.719-1.8230.162090.1274213X-RAY DIFFRACTION99.9774
1.823-1.9490.1672200.1333965X-RAY DIFFRACTION100
1.949-2.1050.1581830.143699X-RAY DIFFRACTION100
2.105-2.3060.1621960.1273424X-RAY DIFFRACTION100
2.306-2.5780.1651650.1323128X-RAY DIFFRACTION100
2.578-2.9760.1771680.1342756X-RAY DIFFRACTION100
2.976-3.6440.1691370.1362382X-RAY DIFFRACTION100
3.644-5.150.1681060.1451895X-RAY DIFFRACTION100

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