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- PDB-9kf8: Crystal structure of ferritin mutant (E53H/E57H/E60H/R64H) -

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Basic information

Entry
Database: PDB / ID: 9kf8
TitleCrystal structure of ferritin mutant (E53H/E57H/E60H/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: 1.501 Å
AuthorsTian, J. / Maity, B. / 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)21,70720
Polymers19,8801
Non-polymers1,82619
Water4,792266
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)520,957480
Polymers477,13224
Non-polymers43,826456
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 area110170 Å2
ΔGint-221 kcal/mol
Surface area143310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.930, 180.930, 180.930
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-604-

CD

21A-605-

CD

31A-607-

CD

41A-947-

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: 19880.480 Da / Num. of mol.: 1 / Mutation: E53H/E57H/E60H/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, 285 molecules

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


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


Mass: 112.411 Da / Num. of mol.: 10 / 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.: 266 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Precipitant: (NH4)2SO4 (0.5-1.0M), CdSO4(12-20mM) Protein: 15-20mg/ml Crystallization drop: 1:1

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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 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.543 Å / Relative weight: 1
ReflectionResolution: 1.5→20.24 Å / Num. obs: 41042 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.033 / Net I/σ(I): 21.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1994 / CC1/2: 0.819 / Rpim(I) all: 0.276 / Rrim(I) all: 0.671 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0425refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.501→20.237 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.963 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1706 1988 4.854 %
Rwork0.1564 38967 -
all0.157 --
obs-40955 99.905 %
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: 10.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.501→20.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 48 266 1713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121551
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161469
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.8472107
X-RAY DIFFRACTIONr_angle_other_deg0.6591.7833387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6025200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.032512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11610283
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.8621081
X-RAY DIFFRACTIONr_chiral_restr0.0910.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021851
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_nbd_refined0.2520.2351
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21223
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2735
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2777
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2181
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2570.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3520.229
X-RAY DIFFRACTIONr_nbd_other0.1680.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3470.24
X-RAY DIFFRACTIONr_mcbond_it1.4140.891729
X-RAY DIFFRACTIONr_mcbond_other1.390.891729
X-RAY DIFFRACTIONr_mcangle_it2.3731.587919
X-RAY DIFFRACTIONr_mcangle_other2.3721.593920
X-RAY DIFFRACTIONr_scbond_it2.5781.217822
X-RAY DIFFRACTIONr_scbond_other2.4011.181803
X-RAY DIFFRACTIONr_scangle_it3.9442.0791176
X-RAY DIFFRACTIONr_scangle_other3.7962.0081147
X-RAY DIFFRACTIONr_lrange_it6.44614.7691936
X-RAY DIFFRACTIONr_lrange_other6.19812.1921839
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
1.501-1.540.1971610.21427910.21329520.9730.971000.179
1.54-1.5820.1821100.227700.228800.9760.9731000.168
1.582-1.6270.191400.19226600.19228000.9770.9751000.156
1.627-1.6770.1711310.17725990.17727300.980.9791000.143
1.677-1.7320.1951450.1724980.17126430.9750.9821000.136
1.732-1.7920.1691160.16624590.16625750.9820.9821000.132
1.792-1.8590.161130.15723700.15724830.9850.9841000.125
1.859-1.9340.171170.15322640.15423810.9820.9851000.125
1.934-2.020.1781170.15121900.15223070.9840.9861000.122
2.02-2.1170.1581220.13620950.13722170.9870.9891000.111
2.117-2.230.167920.13220040.13320960.9830.991000.111
2.23-2.3640.15810.13319290.13420100.9860.9891000.113
2.364-2.5240.182900.1318050.13218960.9820.9999.94730.111
2.524-2.7230.156870.13316850.13417730.9850.98999.94360.114
2.723-2.9780.153740.13515640.13616380.9870.9891000.118
2.978-3.320.138720.14514250.14514980.9890.98799.93320.131
3.32-3.8170.167640.14612840.14713480.9840.9871000.138
3.817-4.6340.164690.15110930.15111620.9820.9861000.149
4.634-6.3870.211650.2058840.2059500.980.9899.89470.2
6.387-20.2370.221220.2265980.2266210.970.96999.8390.222

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