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- PDB-9kkp: Crystal structure of Horse spleen L-ferritin mutant (E53F/E56F/E5... -

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Basic information

Entry
Database: PDB / ID: 9kkp
TitleCrystal structure of Horse spleen L-ferritin mutant (E53F/E56F/E57F/R59F/E60F/E63F) with Nile Red
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / 24mer cage / Phenyl Alanine mutant / Nile red
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: 1.6 Å
AuthorsSuzuki, T. / Hishikawa, Y. / Maity, B. / Abe, S. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Adv Sci / Year: 2025
Title: Design of Aromatic Interaction Networks in a Protein Cage Modulated by Fluorescent Ligand Binding.
Authors: Hishikawa, Y. / Suzuki, T. / Maity, B. / Noya, H. / Yoshizawa, M. / Asanuma, A. / Katagiri, Y. / Abe, S. / Nagatoishi, S. / Tsumoto, K. / Ueno, T.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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)21,26313
Polymers19,9531
Non-polymers1,31112
Water3,351186
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)510,318312
Polymers478,86524
Non-polymers31,453288
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 area119240 Å2
ΔGint-457 kcal/mol
Surface area130470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.511, 181.511, 181.511
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-202-

CD

21A-204-

CD

31A-205-

CD

41A-212-

A1L52

51A-212-

A1L52

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19952.709 Da / Num. of mol.: 1 / Mutation: E53F/E56F/E57F/R59F/E60F/E63F
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 , 6 types, 198 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Chemical ChemComp-A1L52 / Nile Red / 9-(diethylamino)benzo[a]phenoxazin-5-one / Nile Blue A Oxazone


Mass: 318.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18N2O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Ammonium sulfate, Cadmium sulfate / Temp details: Incubation

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Data collection

DiffractionMean temperature: 93 K / Ambient temp details: Liquid N2 vapour / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.6→17.8 Å / Num. obs: 34271 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.017 / Rrim(I) all: 0.057 / Χ2: 0.98 / Net I/σ(I): 29.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1662 / CC1/2: 0.904 / Rpim(I) all: 0.217 / Rrim(I) all: 0.559 / Χ2: 0.93 / % possible all: 100

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Processing

Software
NameVersionClassification
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.6→17.799 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.223 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1858 1708 5.006 %
Rwork0.164 32413 -
all0.165 --
obs-34121 99.429 %
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: 1.6→17.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 48 186 1614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121561
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161487
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.8332121
X-RAY DIFFRACTIONr_angle_other_deg0.6841.7543404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.815197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.1315.38513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91910265
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.9991080
X-RAY DIFFRACTIONr_chiral_restr0.0950.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02418
X-RAY DIFFRACTIONr_nbd_refined0.2450.2338
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.21183
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2745
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2783
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2104
X-RAY DIFFRACTIONr_metal_ion_refined0.3670.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3310.230
X-RAY DIFFRACTIONr_nbd_other0.1350.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.240
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4460.24
X-RAY DIFFRACTIONr_mcbond_it1.5091.137725
X-RAY DIFFRACTIONr_mcbond_other1.4871.136725
X-RAY DIFFRACTIONr_mcangle_it2.3412.029914
X-RAY DIFFRACTIONr_mcangle_other2.342.033915
X-RAY DIFFRACTIONr_scbond_it2.6481.405836
X-RAY DIFFRACTIONr_scbond_other2.6461.405837
X-RAY DIFFRACTIONr_scangle_it3.9932.4391195
X-RAY DIFFRACTIONr_scangle_other3.9912.4391196
X-RAY DIFFRACTIONr_lrange_it5.34515.4761997
X-RAY DIFFRACTIONr_lrange_other5.34315.481998
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
1.6-1.6410.2561020.21623510.21724530.960.9711000.178
1.641-1.6860.2211110.20223020.20324130.9710.9741000.165
1.686-1.7340.2281100.1922340.19223440.9680.9771000.154
1.734-1.7870.2431250.18621430.18922680.9630.9781000.149
1.787-1.8450.1951120.17720770.17821900.9770.98199.95430.139
1.845-1.9090.222920.17520540.17721460.9680.9821000.137
1.909-1.980.21140.17719600.17920800.9750.98199.71150.138
1.98-2.060.168970.16919030.16920040.9830.98399.80040.136
2.06-2.150.186950.15718010.15819080.9810.98599.37110.127
2.15-2.2540.1721110.14217310.14318560.9830.98899.24570.115
2.254-2.3740.176860.13916690.14117650.9830.98899.43340.113
2.374-2.5150.157910.13615800.13716780.9840.98999.58280.114
2.515-2.6850.176810.13714680.13915650.9820.98998.97760.112
2.685-2.8940.165740.1414030.14114910.9850.98899.0610.117
2.894-3.1620.173830.14612820.14713800.9810.98798.9130.127
3.162-3.5210.169600.16811890.16912580.9820.98399.28460.154
3.521-4.040.15550.16110750.16111430.9870.98598.86260.151
4.04-4.8850.191420.1479150.1499690.9830.98798.76160.141
4.885-6.6630.227400.2147640.2158080.9650.97799.50490.201
6.663-17.7990.225270.2125120.2135470.9780.9798.53750.206

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