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- PDB-8j0y: Crystal structure of horse spleen L-ferritin at 20deg Celsius. -

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Basic information

Entry
Database: PDB / ID: 8j0y
TitleCrystal structure of horse spleen L-ferritin at 20deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / 20deg Celsius
Function / homology
Function and homology information


ferritin complex / autolysosome / intracellular sequestering of iron ion / autophagosome / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasmic vesicle / 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
AuthorsMaity, B. / Tian, J. / Abe, S. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Cryst.Growth Des. / Year: 2023
Title: Atomic-Level Insights into a Unique Semi-Clathrate Hydrate Formed in a Confined Environment of Porous Protein Crystal.
Authors: Maity, B. / Tian, J. / Furuta, T. / Abe, S. / Ueno, T.
History
DepositionApr 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4377
Polymers19,8721
Non-polymers5656
Water2,432135
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)490,494168
Polymers476,93824
Non-polymers13,555144
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 area101320 Å2
ΔGint-1081 kcal/mol
Surface area138930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.529, 183.529, 183.529
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
11X-203-

CD

21X-204-

CD

31X-205-

CD

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Components

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Plasmid: PMK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Temp details: No shaking incubation.

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.542 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.6→22.432 Å / Num. obs: 35274 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.057 / Rrim(I) all: 0.132 / Net I/σ(I): 6.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1740 / CC1/2: 0.263 / Rpim(I) all: 1.232 / Rrim(I) all: 2.234 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CrysalisProv42data collection
CrysalisProv42data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
REFMAC5.8.0403refinement
Coot0.9.8.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→22.432 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.92 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1901 1810 5.133 %
Rwork0.1686 33451 -
all0.17 --
obs-35261 99.475 %
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: 18.727 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 14 135 1534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121483
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161408
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.6452012
X-RAY DIFFRACTIONr_angle_other_deg0.5551.5773240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4695192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.072514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29310274
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.3151080
X-RAY DIFFRACTIONr_chiral_restr0.0830.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_nbd_refined0.2410.2291
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.21071
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2720
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2798
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.259
X-RAY DIFFRACTIONr_metal_ion_refined0.2460.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3510.210
X-RAY DIFFRACTIONr_nbd_other0.1780.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.227
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2460.24
X-RAY DIFFRACTIONr_mcbond_it2.0221.604711
X-RAY DIFFRACTIONr_mcbond_other2.0211.605711
X-RAY DIFFRACTIONr_mcangle_it3.1042.863892
X-RAY DIFFRACTIONr_mcangle_other3.1022.872893
X-RAY DIFFRACTIONr_scbond_it4.422.176772
X-RAY DIFFRACTIONr_scbond_other4.3562.147765
X-RAY DIFFRACTIONr_scangle_it6.9463.7351110
X-RAY DIFFRACTIONr_scangle_other6.9333.6751099
X-RAY DIFFRACTIONr_lrange_it8.35818.911687
X-RAY DIFFRACTIONr_lrange_other8.21517.9891666
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
1.6-1.6410.361310.32923590.33125560.8870.8997.41780.328
1.641-1.6860.2811120.3123390.30924820.920.91798.7510.308
1.686-1.7350.2871320.29822820.29824320.9350.93199.25990.295
1.735-1.7880.2861090.2822360.2823540.930.94299.61770.27
1.788-1.8460.2261200.24221580.24122840.9640.95899.73730.227
1.846-1.910.2671280.21620900.21922200.9480.96799.90990.199
1.91-1.9820.22970.20520390.20621370.970.97299.95320.183
1.982-2.0620.2091030.17919770.1820820.9710.97899.90390.154
2.062-2.1530.202980.1618770.16219790.9720.98499.79790.136
2.153-2.2570.1811030.1518130.15219190.9780.98699.84370.13
2.257-2.3780.167850.13317270.13518140.980.98999.88970.117
2.378-2.520.181990.13616280.13917270.980.9881000.118
2.52-2.6920.146910.12815500.12916410.9870.991000.112
2.692-2.9040.172850.12614480.12915360.9810.9999.80470.112
2.904-3.1760.184750.12413510.12714280.9790.9999.85990.112
3.176-3.5420.181680.13612270.13912960.980.98899.92280.125
3.542-4.0730.141550.12511040.12611620.9890.99199.74180.122
4.073-4.9480.132500.1189570.11910100.9880.99199.7030.119
4.948-6.8330.156490.1877710.1858200.9810.9811000.181
6.833-22.4320.184200.1965180.1955420.9770.97599.2620.204

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