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- PDB-9kf7: Crystal structure of ferritin mutant (R52H/E56H/R59H/E63H) -

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Basic information

Entry
Database: PDB / ID: 9kf7
TitleCrystal structure of ferritin mutant (R52H/E56H/R59H/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. / 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)20,97513
Polymers19,8521
Non-polymers1,12212
Water4,738263
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)503,391312
Polymers476,45824
Non-polymers26,934288
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 area114750 Å2
ΔGint-1177 kcal/mol
Surface area140220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.700, 181.700, 181.700
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-603-

CD

21A-604-

CD

31A-606-

CD

41A-866-

HOH

51A-940-

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: 19852.400 Da / Num. of mol.: 1 / Mutation: R52H/E56H/R59H/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, 275 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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.: 263 / 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: 3.15 Å3/Da / Density % sol: 60.92 %
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: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.543 Å / Relative weight: 1
ReflectionResolution: 1.5→23.67 Å / Num. obs: 41552 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.095 / Net I/σ(I): 18.1
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2012 / CC1/2: 0.76 / Rpim(I) all: 0.468 / % 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→23.655 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.1 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1868 2111 5.087 %
Rwork0.1683 39387 -
all0.169 --
obs-41498 99.8 %
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: 10.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 30 263 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151386
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.6272007
X-RAY DIFFRACTIONr_angle_other_deg1.6371.5813191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6785187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97522.75987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60415261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.952159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
X-RAY DIFFRACTIONr_nbd_refined0.2540.2358
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.21259
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2718
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2168
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2910.223
X-RAY DIFFRACTIONr_nbd_other0.1890.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2340.236
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1190.21
X-RAY DIFFRACTIONr_mcbond_it1.150.852706
X-RAY DIFFRACTIONr_mcbond_other1.140.848705
X-RAY DIFFRACTIONr_mcangle_it1.9011.267886
X-RAY DIFFRACTIONr_mcangle_other1.91.272887
X-RAY DIFFRACTIONr_scbond_it2.4321.11772
X-RAY DIFFRACTIONr_scbond_other2.2761.087761
X-RAY DIFFRACTIONr_scangle_it3.6621.5741114
X-RAY DIFFRACTIONr_scangle_other3.5591.5351097
X-RAY DIFFRACTIONr_lrange_it5.84312.2141819
X-RAY DIFFRACTIONr_lrange_other5.57211.2071750
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
1.5-1.5390.2611510.22528220.22729800.8820.88499.76510.198
1.539-1.5810.2441300.21828160.21929460.8980.9151000.189
1.581-1.6260.2081290.19727360.19828650.930.9351000.165
1.626-1.6760.1891510.18525840.18527350.9440.941000.154
1.676-1.7310.2151470.18325540.18527010.940.9461000.151
1.731-1.7910.191480.16824560.16926040.9530.9541000.136
1.791-1.8590.2131100.15924120.16125220.9450.9591000.13
1.859-1.9340.2981240.21923010.22224270.90.93499.91760.182
1.934-2.0190.1811350.16422050.16523420.9590.96499.91460.127
2.019-2.1170.1371190.1421280.1422470.9770.9751000.115
2.117-2.2310.1581060.15220200.15321410.9680.96899.29940.117
2.231-2.3650.1931050.18419040.18520250.9560.95399.20990.147
2.365-2.5260.202760.13218430.13419190.9590.9751000.107
2.526-2.7260.146960.13117060.13218020.9730.9771000.108
2.726-2.9820.116740.13915950.13816690.9820.9771000.115
2.982-3.3280.172850.15314320.15415180.9660.97499.93410.131
3.328-3.830.18690.15612970.15713680.9690.97399.85380.134
3.83-4.660.161610.14911040.14911740.9750.97899.23340.133
4.66-6.4660.199620.1968860.1969500.9640.96799.78950.171
6.466-23.6550.228330.2315860.2316230.9570.94899.35790.203

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