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- PDB-9kp7: Crystal structure of Horse spleen L-ferritin mutant (R59F) with N... -

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Basic information

Entry
Database: PDB / ID: 9kp7
TitleCrystal structure of Horse spleen L-ferritin mutant (R59F) 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 / ferrous iron binding / iron ion transport / 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
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 22, 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

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,33115
Polymers19,8621
Non-polymers1,46914
Water4,125229
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)511,946360
Polymers476,69824
Non-polymers35,248336
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 area128640 Å2
ΔGint-622 kcal/mol
Surface area133300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.335, 181.335, 181.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-201-

CD

21A-202-

CD

31A-203-

CD

41A-214-

A1L52

51A-214-

A1L52

61A-485-

HOH

71A-515-

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: 19862.408 Da / Num. of mol.: 1 / Mutation: R59F
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, 243 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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.: 229 / 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: 3.13 Å3/Da / Density % sol: 60.67 %
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 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.5→19.01 Å / Num. obs: 41305 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.021 / Rrim(I) all: 0.069 / Χ2: 0.99 / Net I/σ(I): 23.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2015 / CC1/2: 0.856 / Rpim(I) all: 0.269 / Rrim(I) all: 0.697 / 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: 1.5→19.01 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1964 2082 5.05 %
Rwork0.178 --
obs0.1789 41197 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→19.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 57 229 1673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161557
X-RAY DIFFRACTIONf_angle_d1.7382112
X-RAY DIFFRACTIONf_dihedral_angle_d13.945622
X-RAY DIFFRACTIONf_chiral_restr0.098227
X-RAY DIFFRACTIONf_plane_restr0.008272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.27291330.22412570X-RAY DIFFRACTION100
1.54-1.570.25681180.21522568X-RAY DIFFRACTION100
1.57-1.620.2551430.20392547X-RAY DIFFRACTION100
1.62-1.660.21361380.19932565X-RAY DIFFRACTION100
1.66-1.720.21041350.19152569X-RAY DIFFRACTION100
1.72-1.780.19421270.18442585X-RAY DIFFRACTION100
1.78-1.850.23571370.18242574X-RAY DIFFRACTION100
1.85-1.930.21191310.18022596X-RAY DIFFRACTION100
1.93-2.040.19371220.17962617X-RAY DIFFRACTION100
2.04-2.160.19751530.17032558X-RAY DIFFRACTION100
2.16-2.330.17211320.16892631X-RAY DIFFRACTION100
2.33-2.560.20831430.16962599X-RAY DIFFRACTION99
2.56-2.930.17541480.17022630X-RAY DIFFRACTION100
2.93-3.690.19141500.16472676X-RAY DIFFRACTION100
3.69-19.010.17181720.17512830X-RAY DIFFRACTION99

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