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- PDB-8j0z: Crystal structure of horse spleen L-ferritin at -180deg Celsius c... -

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Basic information

Entry
Database: PDB / ID: 8j0z
TitleCrystal structure of horse spleen L-ferritin at -180deg Celsius cooled from -40deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / -180deg 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)20,92813
Polymers19,8721
Non-polymers1,05612
Water4,576254
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)502,272312
Polymers476,93824
Non-polymers25,333288
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 area92880 Å2
ΔGint-319 kcal/mol
Surface area141900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.760, 180.760, 180.760
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-528-

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, 266 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
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: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 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: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→24.167 Å / Num. obs: 33140 / % possible obs: 98.2 % / Redundancy: 5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.042 / Rrim(I) all: 0.1 / Net I/σ(I): 11.4
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1655 / CC1/2: 0.72 / Rpim(I) all: 0.411 / Rrim(I) all: 0.766

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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→24.167 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.173 / WRfactor Rwork: 0.144 / SU B: 1.573 / SU ML: 0.053 / Average fsc free: 0.9724 / Average fsc work: 0.9785 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2015 1626 4.908 %
Rwork0.1684 31503 -
all0.17 --
obs-33129 97.7 %
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: 11.158 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 37 254 1676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161441
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6522054
X-RAY DIFFRACTIONr_angle_other_deg0.5861.5793312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0885194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.404516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53510278
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.0721084
X-RAY DIFFRACTIONr_chiral_restr0.0820.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_nbd_refined0.240.2345
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.21184
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2717
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3340.226
X-RAY DIFFRACTIONr_nbd_other0.220.2100
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.246
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1380.22
X-RAY DIFFRACTIONr_mcbond_it1.5921.011713
X-RAY DIFFRACTIONr_mcbond_other1.4671.009713
X-RAY DIFFRACTIONr_mcangle_it2.311.803895
X-RAY DIFFRACTIONr_mcangle_other2.311.807896
X-RAY DIFFRACTIONr_scbond_it2.4591.29804
X-RAY DIFFRACTIONr_scbond_other2.4571.293805
X-RAY DIFFRACTIONr_scangle_it3.8512.2271148
X-RAY DIFFRACTIONr_scangle_other3.8492.2311149
X-RAY DIFFRACTIONr_lrange_it5.9314.4661877
X-RAY DIFFRACTIONr_lrange_other5.9314.4791878
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
1.6-1.6410.2711150.23723380.23824530.9490.961000.217
1.641-1.6860.2641190.22222290.22423500.9590.96599.91490.201
1.686-1.7350.2341200.21922070.2223330.9670.96899.74280.195
1.735-1.7880.2181040.20521340.20622510.9710.97199.42250.181
1.788-1.8460.187990.19220880.19222080.9750.97699.04890.163
1.846-1.9110.2161240.18719680.18821230.9720.97898.53980.157
1.911-1.9820.211980.17618860.17720280.9720.9897.83040.148
1.982-2.0630.19970.15518500.15720100.980.98596.86570.13
2.063-2.1540.183980.14917090.1518910.9780.98795.55790.126
2.154-2.2580.187900.14416310.14618280.980.98894.14660.12
2.258-2.3790.168870.13815310.13917420.9830.98892.88170.117
2.379-2.5220.165720.13914700.1416680.9810.98892.4460.118
2.522-2.6940.2680.1413750.14315460.9750.98893.33760.119
2.694-2.9060.177640.14913970.15114740.9810.98699.1180.127
2.906-3.1790.234590.15313040.15613630.9710.9851000.135
3.179-3.5470.17590.15811850.15912440.9840.9861000.145
3.547-4.0810.207410.14710680.14911130.9740.98799.64060.136
4.081-4.9630.171460.1459130.1469630.9830.98699.58460.134
4.963-6.8750.271400.247350.2417820.9650.97299.10490.218
6.875-24.1670.235260.2234850.2245170.9610.96998.83950.224

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