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- PDB-9kfa: Crystal structure of ferritin mutantFr-H8 (R52H/E53H/E56H/E57H/R5... -

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Basic information

Entry
Database: PDB / ID: 9kfa
TitleCrystal structure of ferritin mutantFr-H8 (R52H/E53H/E56H/E57H/R59H/E60H/E63H/R64H)
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / 24-mer ferritin cage Histidine 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: 1.5 Å
AuthorsTian, J. / Maity, B. / Furuta, T. / Pan, T. / Abe, S. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: An Artificial Metal-Free Peroxidase Designed Using a Ferritin Cage for Bioinspired Catalysis.
Authors: Tian, J. / Maity, B. / Furuta, T. / Pan, T. / Ueno, T.
History
DepositionNov 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 8, 2025Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

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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)21,04913
Polymers19,8601
Non-polymers1,18912
Water4,684260
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)505,185312
Polymers476,65124
Non-polymers28,534288
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 area106300 Å2
ΔGint-873 kcal/mol
Surface area145640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.999, 181.999, 181.999
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-201-

CD

21A-204-

CD

31A-205-

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: 19860.453 Da / Num. of mol.: 1 / Mutation: R52H/E53H/E56H/E57H/R59H/E60H/E63H/R64H
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, 272 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Precipitant: (NH4)2SO4 (0.5-1.0M), CdSO4(12-20mM) Protein: 15-20mg/ml Crystallization drop: 1:1
Temp details: Incubation

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Data collection

DiffractionMean temperature: 93 K / Ambient temp details: Liquid nitrogen vapor / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.543 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.543 Å / Relative weight: 1
ReflectionResolution: 1.5→22.26 Å / Num. obs: 41576 / % possible obs: 99.5 % / Redundancy: 9.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.032 / Rrim(I) all: 0.099 / Net I/σ(I): 17.3
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1744 / CC1/2: 0.797 / Rpim(I) all: 0.376 / Rrim(I) all: 0.96 / % possible all: 100

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Processing

Software
NameVersionClassification
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→22.235 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.413 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2424 2089 5.048 %
Rwork0.2158 39295 -
all0.217 --
obs-41384 99.107 %
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: 13.528 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 23 260 1674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131504
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151393
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.6232040
X-RAY DIFFRACTIONr_angle_other_deg1.6361.5823206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7645188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84322.27388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13815262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.426159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
X-RAY DIFFRACTIONr_nbd_refined0.2610.2370
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.21244
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2719
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2163
X-RAY DIFFRACTIONr_metal_ion_refined0.090.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.219
X-RAY DIFFRACTIONr_nbd_other0.1830.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.010.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0780.22
X-RAY DIFFRACTIONr_mcbond_it1.3151.118719
X-RAY DIFFRACTIONr_mcbond_other1.3141.114718
X-RAY DIFFRACTIONr_mcangle_it2.1611.667906
X-RAY DIFFRACTIONr_mcangle_other2.161.671907
X-RAY DIFFRACTIONr_scbond_it2.5781.449784
X-RAY DIFFRACTIONr_scbond_other2.421.422777
X-RAY DIFFRACTIONr_scangle_it4.092.0641130
X-RAY DIFFRACTIONr_scangle_other3.8632.021119
X-RAY DIFFRACTIONr_lrange_it5.85115.5311845
X-RAY DIFFRACTIONr_lrange_other5.61614.6011792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.251450.24228430.24329890.8740.88199.96650.228
1.539-1.5810.2541550.22628120.22829680.8860.88999.96630.21
1.581-1.6270.2541500.20626860.20928360.8990.9081000.183
1.627-1.6760.2081290.20726560.20727860.9330.92399.96410.182
1.676-1.7310.2751400.19725440.20126840.9030.931000.171
1.731-1.7920.2091400.18825050.18926450.9370.9411000.16
1.792-1.8590.2221260.18823890.1925150.9350.9421000.158
1.859-1.9340.5551310.53122270.53224470.6960.71596.36290.481
1.934-2.0190.3191160.31221430.31223330.8670.8796.82810.226
2.019-2.1170.181050.16221650.16322700.9590.9651000.135
2.117-2.230.3561010.27219730.27521550.8950.91496.24130.192
2.23-2.3640.3381110.35118380.3520260.8440.8396.19940.274
2.364-2.5250.221930.14118450.14519380.9540.9671000.119
2.525-2.7250.205890.14516990.14817900.9590.96999.88830.122
2.725-2.980.162890.14115880.14216800.970.97499.82140.119
2.98-3.3250.165760.14914420.1515200.9680.97599.86840.13
3.325-3.8250.175710.17612890.17613700.9660.96899.27010.15
3.825-4.650.153510.1611370.1611920.9750.97299.66440.144
4.65-6.4370.22400.1969200.1979610.9630.96899.89590.176
6.437-22.2350.219310.2415940.246260.9580.9599.84030.216

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