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- PDB-8j0w: Crystal structure of horse spleen L-ferritin at -40deg Celsius. -

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Basic information

Entry
Database: PDB / ID: 8j0w
TitleCrystal structure of horse spleen L-ferritin at -40deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / -40deg 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)20,65710
Polymers19,8721
Non-polymers7859
Water3,423190
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)495,779240
Polymers476,93824
Non-polymers18,840216
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_556-y,-x,-z+11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_545y,z-1/2,x+1/21
crystal symmetry operation34_545-y,z-1/2,-x+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation36_555-y,-z+1/2,x+1/21
crystal symmetry operation41_545x,z-1/2,-y+1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_555-x,-z+1/2,-y+1/21
crystal symmetry operation44_555x,-z+1/2,y+1/21
crystal symmetry operation53_455z-1/2,x,y+1/21
crystal symmetry operation54_455z-1/2,-x,-y+1/21
crystal symmetry operation55_555-z+1/2,-x,y+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation69_455z-1/2,y,-x+1/21
crystal symmetry operation70_455z-1/2,-y,x+1/21
crystal symmetry operation71_555-z+1/2,y,x+1/21
crystal symmetry operation72_555-z+1/2,-y,-x+1/21
Buried area104280 Å2
ΔGint-140 kcal/mol
Surface area136190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.999, 181.999, 181.999
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-202-

SO4

21X-204-

CD

31X-205-

CD

41X-206-

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

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Non-polymers , 5 types, 199 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.16 Å3/Da / Density % sol: 61.08 %
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: Non shaking incubation

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Data collection

DiffractionMean temperature: 233.15 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→22.245 Å / Num. obs: 34339 / % possible obs: 99.5 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.029 / Rrim(I) all: 0.069 / Net I/σ(I): 14.7
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1644 / CC1/2: 0.801 / Rpim(I) all: 0.303 / Rrim(I) all: 0.539

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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→22.245 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.128 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1752 1742 5.076 %
Rwork0.1453 32577 -
all0.147 --
obs-34319 99.26 %
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: 13.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 27 190 1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121492
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161412
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.6492020
X-RAY DIFFRACTIONr_angle_other_deg0.5951.5783247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9925190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.457514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04710272
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.0031082
X-RAY DIFFRACTIONr_chiral_restr0.090.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
X-RAY DIFFRACTIONr_nbd_refined0.2440.2311
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.21136
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2721
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2802
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2112
X-RAY DIFFRACTIONr_metal_ion_refined0.3040.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.220
X-RAY DIFFRACTIONr_nbd_other0.1810.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.249
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3460.26
X-RAY DIFFRACTIONr_mcbond_it1.8541.13709
X-RAY DIFFRACTIONr_mcbond_other1.8441.129709
X-RAY DIFFRACTIONr_mcangle_it2.9742.017889
X-RAY DIFFRACTIONr_mcangle_other2.9732.024890
X-RAY DIFFRACTIONr_scbond_it3.221.532783
X-RAY DIFFRACTIONr_scbond_other3.221.535784
X-RAY DIFFRACTIONr_scangle_it5.0852.6161122
X-RAY DIFFRACTIONr_scangle_other5.0832.6181123
X-RAY DIFFRACTIONr_lrange_it6.62615.1081776
X-RAY DIFFRACTIONr_lrange_other6.62615.1151777
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
1.6-1.6420.2171210.2123150.2124810.970.97198.18620.18
1.642-1.6860.2291060.19723030.19924390.9670.97498.770.166
1.686-1.7350.2021260.18822040.18823430.9690.97799.44520.158
1.735-1.7880.2151270.17821740.1823140.9720.97999.43820.146
1.788-1.8460.1811130.16320880.16422170.9810.98399.27830.132
1.846-1.910.1571050.14920350.14921640.9860.98698.89090.121
1.91-1.9820.1541000.14219590.14221020.9850.98897.95430.116
1.982-2.0620.144920.13319060.13420050.9870.98999.65090.109
2.062-2.1530.171930.12718470.12919400.9830.991000.107
2.153-2.2570.1631110.12417560.12618700.9840.99199.83960.108
2.257-2.3780.161900.12117060.12317960.9830.9911000.109
2.378-2.520.166860.12415930.12716790.9850.9911000.111
2.52-2.6920.157730.12715090.12915830.9840.9999.93680.114
2.692-2.9040.157710.12614290.12715000.9860.991000.112
2.904-3.1760.157660.13613160.13713830.9850.98999.92770.128
3.176-3.5420.167770.14412030.14512800.9840.9881000.144
3.542-4.0720.19770.12810530.13111330.9790.9999.73520.133
4.072-4.9460.141490.1279400.1289930.9890.9999.59720.136
4.946-6.8280.25420.2027450.2047950.9690.97898.99370.206
6.828-22.2450.269170.1954960.1975320.9640.97696.42860.221

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