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- PDB-7bd7: X-ray structure of Arsenoplatin-1-encapsulated horse spleen ferritin -

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Basic information

Entry
Database: PDB / ID: 7bd7
TitleX-ray structure of Arsenoplatin-1-encapsulated horse spleen ferritin
ComponentsFerritin light chain
KeywordsTRANSPORT PROTEIN / ferritin / drug delivery / metallodrug / arsenoplatin / anticancer
Function / homology
Function and homology information


intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / 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
arsenoplatin-1 / : / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFerraro, G. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer Research22587 Italy
CitationJournal: Int J Mol Sci / Year: 2021
Title: Arsenoplatin-Ferritin Nanocage: Structure and Cytotoxicity.
Authors: Ferraro, G. / Pratesi, A. / Cirri, D. / Imbimbo, P. / Maria Monti, D. / Messori, L. / Merlino, A.
History
DepositionDec 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)22,10824
Polymers19,6191
Non-polymers2,48923
Water3,783210
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)530,596576
Polymers470,86124
Non-polymers59,735552
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation6_676z+1,-x+2,-y+11
crystal symmetry operation7_674-z+1,-x+2,y-11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation10_766-y+2,z+1,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_764-y+2,-z+1,x-11
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_775-y+2,-x+2,-z1
crystal symmetry operation15_575y,-x+2,z1
crystal symmetry operation16_755-y+2,x,z1
crystal symmetry operation17_566x,z+1,-y+11
crystal symmetry operation18_764-x+2,z+1,y-11
crystal symmetry operation19_766-x+2,-z+1,-y+11
crystal symmetry operation20_564x,-z+1,y-11
crystal symmetry operation21_656z+1,y,-x+11
crystal symmetry operation22_674z+1,-y+2,x-11
crystal symmetry operation23_654-z+1,y,x-11
crystal symmetry operation24_676-z+1,-y+2,-x+11
Buried area119080 Å2
ΔGint-1423 kcal/mol
Surface area137520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.910, 180.910, 180.910
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
11A-205-

CD

21A-208-

CD

31A-209-

CD

41A-458-

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: 19619.191 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 , 7 types, 233 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-A6R / arsenoplatin-1


Mass: 418.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8AsN2O4Pt / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.6 M ammomium sulphate 0.1 M Tris HCl buffer pH 7.2 60 mM cadmium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→41.538 Å / Num. obs: 40897 / % possible obs: 100 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.04 / Rrim(I) all: 0.12 / Net I/σ(I): 12.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2028 / CC1/2: 0.563 / Rpim(I) all: 0.404 / Rrim(I) all: 0.891 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5erk

5erk


Resolution: 1.5→41.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.169 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 2059 5 %RANDOM
Rwork0.1663 ---
obs0.1673 38816 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.31 Å2 / Biso mean: 17.101 Å2 / Biso min: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.5→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 47 210 1636
Biso mean--51.21 34.34 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131453
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171342
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.6491962
X-RAY DIFFRACTIONr_angle_other_deg1.6311.5793108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7015177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90422.18487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28315263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4851512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02314
LS refinement shellResolution: 1.502→1.541 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 145 -
Rwork0.278 2825 -
all-2970 -
obs--100 %

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