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- PDB-5erk: X-ray structure of horse spleen apoferritin (control) -

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Basic information

Entry
Database: PDB / ID: 5erk
TitleX-ray structure of horse spleen apoferritin (control)
ComponentsFerritin light chain
KeywordsMETAL TRANSPORT / protein nanocage
Function / homology
Function and homology information


ferritin complex / autolysosome / intracellular sequestering of iron ion / autophagosome / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasmic vesicle / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPontillo, N. / Merlino, A.
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: Cisplatin encapsulation within a ferritin nanocage: a high-resolution crystallographic study.
Authors: Pontillo, N. / Pane, F. / Messori, L. / Amoresano, A. / Merlino, A.
History
DepositionNov 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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)21,72020
Polymers19,8721
Non-polymers1,84819
Water3,531196
1
A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules

A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)521,289480
Polymers476,93824
Non-polymers44,351456
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)180.619, 180.619, 180.619
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-208-

CD

31A-461-

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 , 5 types, 215 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 13 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 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: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.065 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.065 Å / Relative weight: 1
ReflectionResolution: 2→104.28 Å / Num. obs: 17642 / % possible obs: 100 % / Redundancy: 17.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→104.28 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.91 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18071 883 5 %RANDOM
Rwork0.14347 ---
obs0.14527 16759 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.099 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→104.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 33 196 1614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191510
X-RAY DIFFRACTIONr_bond_other_d0.0030.021443
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9662044
X-RAY DIFFRACTIONr_angle_other_deg1.03933313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4835190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53823.95181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10615274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4691513
X-RAY DIFFRACTIONr_chiral_restr0.1140.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021754
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02375
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_it1.9291.694727
X-RAY DIFFRACTIONr_mcbond_other1.8791.689726
X-RAY DIFFRACTIONr_mcangle_it2.8282.514919
X-RAY DIFFRACTIONr_mcangle_other2.8272.518920
X-RAY DIFFRACTIONr_scbond_it3.422.159781
X-RAY DIFFRACTIONr_scbond_other3.4142.159781
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.473.0721122
X-RAY DIFFRACTIONr_long_range_B_refined8.68816.0441933
X-RAY DIFFRACTIONr_long_range_B_other8.68716.0611934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 68 -
Rwork0.192 1206 -
obs--100 %

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