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- PDB-9kf5: Crystal structure of Ferritin mutant(E53H/E57H) -

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Basic information

Entry
Database: PDB / ID: 9kf5
TitleCrystal structure of Ferritin mutant(E53H/E57H)
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,82111
Polymers19,8901
Non-polymers93010
Water4,918273
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)499,695264
Polymers477,37224
Non-polymers22,323240
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 area108300 Å2
ΔGint-456 kcal/mol
Surface area142310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.681, 182.681, 182.681
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-606-

CD

31A-607-

CD

41A-863-

HOH

51A-953-

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: 19890.494 Da / Num. of mol.: 1 / Mutation: E53H/E57H
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, 283 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.: 1 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
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

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.543 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.543 Å / Relative weight: 1
ReflectionResolution: 1.5→23.81 Å / Num. obs: 42036 / % possible obs: 99.4 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.1
Reflection shellResolution: 1.5→1.66 Å / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1599 / CC1/2: 0.796 / Rrim(I) all: 0.769

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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→23.783 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.916 / SU B: 1.569 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2409 2100 5.046 %
Rwork0.2189 39521 -
all0.22 --
obs-41621 98.507 %
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: 12.354 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 20 273 1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131485
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151413
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.6352007
X-RAY DIFFRACTIONr_angle_other_deg1.61.5863248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5055188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51922.17492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71615271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1421512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined0.2540.2362
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.21235
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2717
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2164
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.21
X-RAY DIFFRACTIONr_metal_ion_refined0.240.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3930.210
X-RAY DIFFRACTIONr_nbd_other0.1620.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.229
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0680.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2170.24
X-RAY DIFFRACTIONr_mcbond_it1.1230.984713
X-RAY DIFFRACTIONr_mcbond_other1.0960.974711
X-RAY DIFFRACTIONr_mcangle_it1.8161.465896
X-RAY DIFFRACTIONr_mcangle_other1.8121.464896
X-RAY DIFFRACTIONr_scbond_it2.3271.264771
X-RAY DIFFRACTIONr_scbond_other2.3171.257768
X-RAY DIFFRACTIONr_scangle_it3.6211.7871104
X-RAY DIFFRACTIONr_scangle_other3.6281.7731099
X-RAY DIFFRACTIONr_lrange_it6.28314.0051832
X-RAY DIFFRACTIONr_lrange_other5.98912.8371766
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
1.5-1.5390.281530.26929160.26930720.8140.82999.90230.257
1.539-1.5810.2721510.25228140.25329650.8330.8491000.238
1.581-1.6270.2651530.23627250.23828780.8740.8741000.219
1.627-1.6760.2321320.21927100.21928420.9030.8961000.196
1.676-1.7310.2241450.20725770.20827220.910.9131000.183
1.731-1.7920.241400.19425080.19726480.9180.9281000.168
1.792-1.8590.2031240.18324220.18425460.9340.9341000.158
1.859-1.9340.551270.5421410.54124710.5950.60391.78470.513
1.934-2.020.3411180.28621440.28923800.8730.89395.0420.217
2.02-2.1170.156990.1521860.1522850.9690.9721000.129
2.117-2.2310.2831020.26619260.26721700.8850.88793.45620.194
2.231-2.3650.3591050.38518430.38320560.8090.79294.74710.323
2.365-2.5260.16980.12618450.12719430.9640.9731000.106
2.526-2.7260.171890.1317530.13218420.9680.9761000.107
2.726-2.9830.185900.13515980.13816880.9620.9721000.114
2.983-3.3280.165760.1514670.15115440.9710.97199.93520.128
3.328-3.8310.187750.19212870.19113880.9550.95698.12680.162
3.831-4.6610.15510.14911430.14911990.9760.97599.5830.13
4.661-6.4690.268410.1919200.1949610.9390.9661000.167
6.469-23.7830.158310.2075950.2036270.9780.96199.84050.176

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