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- PDB-9kf9: Crystal structure of ferritin mutant(E53H/E56H/E57H/R59H/E60H/E63H) -

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Basic information

Entry
Database: PDB / ID: 9kf9
TitleCrystal structure of ferritin mutant(E53H/E56H/E57H/R59H/E60H/E63H)
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. / 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)20,70110
Polymers19,8991
Non-polymers8039
Water4,918273
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)496,829240
Polymers477,56524
Non-polymers19,264216
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 area97000 Å2
ΔGint-223 kcal/mol
Surface area141660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.639, 181.639, 181.639
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-602-

CD

21A-603-

CD

31A-725-

HOH

41A-932-

HOH

51A-945-

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: 19898.547 Da / Num. of mol.: 1 / Mutation: E53H/E56H/E57H/R59H/E60H/E63H
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, 282 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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.: 273 / 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: 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→22.23 Å / Num. obs: 41233 / % possible obs: 99.3 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.033 / Rrim(I) all: 0.092 / Net I/σ(I): 17
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2016 / CC1/2: 0.82 / Rpim(I) all: 0.31 / Rrim(I) all: 0.698 / % possible all: 99.6

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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→22.191 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.915 / SU B: 1.209 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2251 2055 5.035 %
Rwork0.2066 38758 -
all0.208 --
obs-40813 98.219 %
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: 10.649 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 32 273 1692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131491
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151406
X-RAY DIFFRACTIONr_angle_refined_deg1.831.6282021
X-RAY DIFFRACTIONr_angle_other_deg1.6531.5863233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6035187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59222.02289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33115269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.81511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021692
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02362
X-RAY DIFFRACTIONr_nbd_refined0.2570.2362
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.21266
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2702
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2646
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.21
X-RAY DIFFRACTIONr_metal_ion_refined0.3580.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2750.227
X-RAY DIFFRACTIONr_nbd_other0.2070.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.237
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4070.23
X-RAY DIFFRACTIONr_mcbond_it1.2030.811703
X-RAY DIFFRACTIONr_mcbond_other1.1090.807702
X-RAY DIFFRACTIONr_mcangle_it1.8851.207881
X-RAY DIFFRACTIONr_mcangle_other1.8851.212882
X-RAY DIFFRACTIONr_scbond_it2.4041.137787
X-RAY DIFFRACTIONr_scbond_other2.2661.088768
X-RAY DIFFRACTIONr_scangle_it3.7791.6061132
X-RAY DIFFRACTIONr_scangle_other3.5821.5261103
X-RAY DIFFRACTIONr_lrange_it5.8311.941820
X-RAY DIFFRACTIONr_lrange_other5.62610.8551750
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
1.5-1.5390.2551370.22828570.22930000.8910.90399.80.2
1.539-1.5810.2321560.2127650.21129210.9160.9181000.179
1.581-1.6270.1811530.19226900.19128440.9420.93699.96480.161
1.627-1.6760.1961260.17826250.17927520.950.94599.96370.145
1.676-1.7310.2131370.17725600.17926970.9350.9491000.147
1.731-1.7910.1861440.16124540.16325980.9550.9561000.132
1.791-1.8580.1781240.16623980.16725230.9490.9599.96040.139
1.858-1.9340.5021250.51920630.51824120.6920.69290.71310.459
1.934-2.0190.261060.29120840.28923410.9170.91293.54980.201
2.019-2.1170.1631030.14421470.14522500.9690.9731000.12
2.117-2.230.2851000.25819170.25921310.8620.87794.65040.178
2.23-2.3640.3921070.35917750.36120250.7660.79792.93830.282
2.364-2.5250.158930.13118260.13219190.9680.9721000.109
2.525-2.7240.139880.12817060.12917940.9710.9781000.108
2.724-2.980.144890.13415810.13516700.9760.9771000.112
2.98-3.3240.172760.15114420.15215180.9660.9721000.133
3.324-3.8240.197680.17412530.17613660.960.96696.70570.147
3.824-4.6490.16510.15111090.15111740.9750.97498.80750.135
4.649-6.4350.249410.1979120.1999530.9510.9661000.176
6.435-22.1910.186310.225930.2176250.9720.9699.840.196

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