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- PDB-21lp: Crystal structure of Horse spleen L-ferritin mutant (L24G/S27G/E5... -

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Basic information

Entry
Database: PDB / ID: 21lp
TitleCrystal structure of Horse spleen L-ferritin mutant (L24G/S27G/E56F/R59G/E60F/E63F)
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / 24mer cage / Phenylalanine mutant / Glycine mutant
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 / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsSuzuki, T. / Hishikawa, Y. / Maity, B. / Abe, S. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Chem.Commun.(Camb.) / Year: 2026
Title: Design of a flexible aromatic gate to immobilize C 60 in a ferritin cage.
Authors: Suzuki, T. / Hishikawa, Y. / Maity, B. / Nishiyama, Y. / Motai, K. / Hayamizu, Y. / Abe, S. / Ueno, T.
History
DepositionDec 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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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)20,71612
Polymers19,7401
Non-polymers97611
Water4,017223
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)497,188288
Polymers473,76824
Non-polymers23,420264
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area110840 Å2
ΔGint-795 kcal/mol
Surface area143360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.150, 181.150, 181.150
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-205-

CD

31A-206-

CD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19740.332 Da / Num. of mol.: 1 / Mutation: L24G/S27G/E56F/R59G/E60F/E63F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Escherichia coli (E. coli) / References: UniProt: P02791

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Non-polymers , 5 types, 234 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Ammonium sulfate, Cadmium sulfate / Temp details: Incubation

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Data collection

DiffractionMean temperature: 93 K / Ambient temp details: Liquid N2 vapour / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.57→22.13 Å / Num. obs: 36031 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.022 / Rrim(I) all: 0.074 / Χ2: 0.98 / Net I/σ(I): 23.4
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1742 / CC1/2: 0.831 / Rpim(I) all: 0.312 / Rrim(I) all: 0.866 / Χ2: 0.91 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→22.13 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 1706 4.78 %
Rwork0.1938 --
obs0.1948 35709 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→22.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 28 223 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081504
X-RAY DIFFRACTIONf_angle_d0.9942038
X-RAY DIFFRACTIONf_dihedral_angle_d14.552577
X-RAY DIFFRACTIONf_chiral_restr0.051217
X-RAY DIFFRACTIONf_plane_restr0.012268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.620.27961180.24242823X-RAY DIFFRACTION100
1.62-1.670.24281460.22412790X-RAY DIFFRACTION100
1.67-1.730.27471040.21712838X-RAY DIFFRACTION100
1.73-1.80.21851350.21772797X-RAY DIFFRACTION100
1.8-1.880.22511520.21332804X-RAY DIFFRACTION100
1.88-1.980.2281550.21472796X-RAY DIFFRACTION99
1.98-2.10.21411470.19732813X-RAY DIFFRACTION99
2.1-2.260.22671480.18942792X-RAY DIFFRACTION98
2.26-2.490.21931600.18982758X-RAY DIFFRACTION97
2.49-2.850.22921460.1892846X-RAY DIFFRACTION98
2.85-3.590.1711590.1752854X-RAY DIFFRACTION98
3.59-22.130.19791360.18143092X-RAY DIFFRACTION99

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