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- PDB-8j0x: Crystal structure of horse spleen L-ferritin at -20deg Celsius. -

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Basic information

Entry
Database: PDB / ID: 8j0x
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 / 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, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
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

Downloads & links

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Assembly

Deposited unit
X: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6129
Polymers19,8721
Non-polymers7398
Water2,900161
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)494,681216
Polymers476,93824
Non-polymers17,743192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Buried area96740 Å2
ΔGint-554 kcal/mol
Surface area140410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.340, 182.340, 182.340
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-201-

CD

21X-202-

CD

31X-203-

CD

41X-204-

CD

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Components

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Protein , 1 types, 1 molecules X

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791

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Non-polymers , 5 types, 169 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / 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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Temp details: Non-shaking incubation.

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Data collection

DiffractionMean temperature: 253.15 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 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.6→22.286 Å / Num. obs: 34348 / % possible obs: 98.9 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Net I/σ(I): 15.6
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1665 / CC1/2: 0.708 / Rpim(I) all: 0.404 / Rrim(I) all: 0.732

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
CrysalisProv42data collection
CrysalisProv42data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
Coot0.9.8.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→22.286 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.261 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1687 1712 4.986 %
Rwork0.1477 32627 -
all0.149 --
obs-34339 98.684 %
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: 14.359 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 19 161 1565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121488
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161420
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.6472017
X-RAY DIFFRACTIONr_angle_other_deg0.611.5773266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.046514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09610275
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.2561080
X-RAY DIFFRACTIONr_chiral_restr0.0940.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_nbd_refined0.2420.2299
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.21122
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2716
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2710.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3460.221
X-RAY DIFFRACTIONr_nbd_other0.130.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.280.28
X-RAY DIFFRACTIONr_mcbond_it2.2231.218711
X-RAY DIFFRACTIONr_mcbond_other2.2041.218711
X-RAY DIFFRACTIONr_mcangle_it3.2512.171892
X-RAY DIFFRACTIONr_mcangle_other3.2492.177893
X-RAY DIFFRACTIONr_scbond_it4.0191.681777
X-RAY DIFFRACTIONr_scbond_other4.0171.684778
X-RAY DIFFRACTIONr_scangle_it6.0732.8561115
X-RAY DIFFRACTIONr_scangle_other6.072.8581116
X-RAY DIFFRACTIONr_lrange_it7.74414.1661732
X-RAY DIFFRACTIONr_lrange_other7.74314.1651732
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
1.6-1.6410.2711060.22923530.23125090.9510.96398.00720.205
1.641-1.6860.2161120.22422920.22324460.9680.96798.28290.196
1.686-1.7350.2351080.20922230.2123890.9650.9797.57220.18
1.735-1.7880.271190.19721360.223040.9490.97397.87330.167
1.788-1.8460.1991130.17220920.17322500.9760.98980.142
1.846-1.910.179920.16320140.16421570.9790.98397.63560.132
1.91-1.9820.1881090.15819570.1621200.9790.98497.45280.129
1.982-2.0620.171970.1518780.15120120.980.98698.1610.119
2.062-2.1530.154940.13218510.13319710.9850.98998.68090.109
2.153-2.2570.1591140.12317630.12518790.9850.99199.89360.105
2.257-2.3780.134850.11916900.1217750.9880.9911000.1
2.378-2.520.163960.11916150.12117110.9830.9911000.103
2.52-2.6920.137830.11815140.11915970.9880.9921000.101
2.692-2.9040.15730.12514340.12615070.9860.991000.107
2.904-3.1760.138860.12813080.12913940.9870.991000.112
3.176-3.5410.154600.13612200.13712800.9850.9891000.123
3.541-4.0720.119550.12910810.12811370.9910.9999.9120.121
4.072-4.9460.183440.1279520.1299960.9780.991000.123
4.946-6.8290.2380.1837630.1848020.9810.98399.87530.173
6.829-22.2860.189280.1924910.1925350.9840.97797.00930.188

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