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- PDB-5mik: X-ray structure of carboplatin-encapsulated horse spleen apoferri... -

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Basic information

Entry
Database: PDB / ID: 5mik
TitleX-ray structure of carboplatin-encapsulated horse spleen apoferritin (rotating anode 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 / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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: 1.96 Å
AuthorsPontillo, N. / Ferraro, G. / Helliwell, J.R. / Merlino, A.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: X-ray Structure of the Carboplatin-Loaded Apo-Ferritin Nanocage.
Authors: Pontillo, N. / Ferraro, G. / Helliwell, J.R. / Amoresano, A. / Merlino, A.
History
DepositionNov 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)21,88620
Polymers19,8721
Non-polymers2,01319
Water3,423190
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)525,257480
Polymers476,93824
Non-polymers48,319456
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)180.654, 180.654, 180.654
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-206-

CD

31A-413-

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, 209 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 60.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 0.8 M (NH4)2SO4, 0.1 M Tris pH 7.7, 60 mM CdSO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 10, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→104.3 Å / Num. obs: 18700 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.2
Reflection shellResolution: 1.96→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5erk

5erk


Resolution: 1.96→104.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.795 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19161 904 4.8 %RANDOM
Rwork0.14623 ---
obs0.14847 17792 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.803 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.96→104.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 33 190 1609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191548
X-RAY DIFFRACTIONr_bond_other_d0.0020.021474
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9682101
X-RAY DIFFRACTIONr_angle_other_deg1.02833391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8124.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99815284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.431514
X-RAY DIFFRACTIONr_chiral_restr0.1110.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
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_it1.871.73743
X-RAY DIFFRACTIONr_mcbond_other1.8661.726742
X-RAY DIFFRACTIONr_mcangle_it2.7622.57943
X-RAY DIFFRACTIONr_mcangle_other2.762.575944
X-RAY DIFFRACTIONr_scbond_it2.8872.113803
X-RAY DIFFRACTIONr_scbond_other2.8722.113803
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5233.0281152
X-RAY DIFFRACTIONr_long_range_B_refined7.61215.5111968
X-RAY DIFFRACTIONr_long_range_B_other7.6115.5281969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 65 -
Rwork0.199 1295 -
obs--100 %

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