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- PDB-8j0v: Crystal structure of horse spleen L-ferritin at -100deg Celsius. -

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Basic information

Entry
Database: PDB / ID: 8j0v
TitleCrystal structure of horse spleen L-ferritin at -100deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / -100deg 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)20,87813
Polymers19,8721
Non-polymers1,00512
Water4,360242
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)501,063312
Polymers476,93824
Non-polymers24,125288
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 area101240 Å2
ΔGint-913 kcal/mol
Surface area135230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.624, 180.624, 180.624
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-205-

CD

21X-206-

CD

31X-520-

HOH

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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 / Plasmid: PMK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791

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Non-polymers , 5 types, 254 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 96.063 Da / Num. of mol.: 4 / 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.: 242 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)

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Data collection

DiffractionMean temperature: 173.15 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: Dec 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.6→23.526 Å / Num. obs: 34683 / % possible obs: 99.7 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.046 / Rrim(I) all: 0.109 / Net I/σ(I): 10.6
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1621 / CC1/2: 0.508 / Rpim(I) all: 0.628 / Rrim(I) all: 1.203

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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→23.526 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.16 / WRfactor Rwork: 0.143 / SU B: 1.631 / SU ML: 0.054 / Average fsc free: 0.9714 / Average fsc work: 0.9741 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1905 1642 4.883 %
Rwork0.1714 31986 -
all0.172 --
obs-33628 99.459 %
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: 14.372 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 40 242 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161395
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.651996
X-RAY DIFFRACTIONr_angle_other_deg0.5991.5783204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7675184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.084513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50810265
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.0771080
X-RAY DIFFRACTIONr_chiral_restr0.090.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021761
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02359
X-RAY DIFFRACTIONr_nbd_refined0.2450.2333
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.21177
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2714
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3290.240
X-RAY DIFFRACTIONr_nbd_other0.2390.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.252
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1470.22
X-RAY DIFFRACTIONr_mcbond_it1.6181.304703
X-RAY DIFFRACTIONr_mcbond_other1.6171.303703
X-RAY DIFFRACTIONr_mcangle_it2.4742.324880
X-RAY DIFFRACTIONr_mcangle_other2.4762.33881
X-RAY DIFFRACTIONr_scbond_it3.0631.667777
X-RAY DIFFRACTIONr_scbond_other3.011.653762
X-RAY DIFFRACTIONr_scangle_it4.7722.8731110
X-RAY DIFFRACTIONr_scangle_other4.7222.841087
X-RAY DIFFRACTIONr_lrange_it6.61618.8311836
X-RAY DIFFRACTIONr_lrange_other6.59418.631822
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
1.6-1.6420.281150.27222670.27324320.9370.94497.94410.261
1.642-1.6860.2411190.26522230.26423720.9550.94998.73520.25
1.686-1.7350.2791170.2621550.26122930.9480.95499.08420.239
1.735-1.7880.2511070.24621330.24722560.9590.95999.29080.223
1.788-1.8460.2241030.21420930.21422060.9660.96999.54670.186
1.846-1.9110.1951050.19819900.19820990.9750.97499.80940.17
1.911-1.9820.202920.17919440.1820380.9770.97999.90190.152
1.982-2.0630.1851090.16618650.16719780.980.98399.79780.139
2.063-2.1540.182890.16218130.16319040.9780.98499.8950.135
2.154-2.2580.184840.1417480.14218340.9790.98899.89090.118
2.258-2.3790.137690.13516700.13517390.9880.9891000.116
2.379-2.5210.137810.13115670.13116480.9880.991000.109
2.521-2.6930.172770.13814820.13915620.9820.98899.80790.115
2.693-2.9060.156670.14113900.14214600.9830.98899.79450.12
2.906-3.1780.166640.14312850.14413510.9880.98899.8520.125
3.178-3.5460.165600.15511880.15512480.9880.9861000.139
3.546-4.0790.17560.14610450.14711070.9840.98799.4580.134
4.079-4.9580.201640.1418970.1449630.9770.98799.79230.13
4.958-6.8610.268460.2347320.2357780.9720.9741000.21
6.861-23.5260.208180.2114990.2115200.9840.97299.42310.199

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