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- PDB-8j0u: Crystal structure of horse spleen L-ferritin A115T mutant at -180... -

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Basic information

Entry
Database: PDB / ID: 8j0u
TitleCrystal structure of horse spleen L-ferritin A115T mutant at -180deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / A115T mutant / -180deg 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: 1.5 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
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,44718
Polymers19,9021
Non-polymers1,54517
Water4,360242
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)514,728432
Polymers477,65924
Non-polymers37,069408
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 area106220 Å2
ΔGint-1234 kcal/mol
Surface area141450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.156, 181.156, 181.156
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
11A-604-

CD

21A-606-

CD

31A-611-

CD

41A-613-

SO4

51A-921-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19902.455 Da / Num. of mol.: 1 / Mutation: A115T
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 , 6 types, 259 molecules

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


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


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: 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: 3.11 Å3/Da / Density % sol: 60.47 %
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: 93.15 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: Jan 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.5→23.596 Å / Num. obs: 41193 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.028 / Rrim(I) all: 0.078 / Net I/σ(I): 19.7
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2003 / CC1/2: 0.742 / Rpim(I) all: 0.336 / Rrim(I) all: 0.748

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
CrysalisProv42data collection
CrysalisProv42data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
Coot0.9.8.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→23.596 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.155 / WRfactor Rwork: 0.134 / SU B: 1.069 / SU ML: 0.039 / Average fsc free: 0.9776 / Average fsc work: 0.9808 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1808 1997 4.851 %
Rwork0.1591 39174 -
all0.16 --
obs-41171 99.925 %
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: 11.409 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 38 242 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121508
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161444
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.6482041
X-RAY DIFFRACTIONr_angle_other_deg0.6311.5773322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7185193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.195514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.310279
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.1851081
X-RAY DIFFRACTIONr_chiral_restr0.0980.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
X-RAY DIFFRACTIONr_nbd_refined0.2560.2347
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21246
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2732
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2827
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.2161
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.22
X-RAY DIFFRACTIONr_metal_ion_refined0.330.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.380.223
X-RAY DIFFRACTIONr_nbd_other0.1480.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.244
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3170.28
X-RAY DIFFRACTIONr_mcbond_it1.7371.017715
X-RAY DIFFRACTIONr_mcbond_other1.7081.017715
X-RAY DIFFRACTIONr_mcangle_it2.6451.811897
X-RAY DIFFRACTIONr_mcangle_other2.6451.819898
X-RAY DIFFRACTIONr_scbond_it2.8261.305793
X-RAY DIFFRACTIONr_scbond_other2.7491.294782
X-RAY DIFFRACTIONr_scangle_it4.4142.2461134
X-RAY DIFFRACTIONr_scangle_other4.3722.221117
X-RAY DIFFRACTIONr_lrange_it6.30514.6531884
X-RAY DIFFRACTIONr_lrange_other6.01212.7651788
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
1.5-1.5390.2051610.22428090.22329740.9680.96699.86550.198
1.539-1.5810.2441130.21827980.21929110.9630.9671000.191
1.581-1.6270.2031390.20526720.20428110.9720.9721000.173
1.627-1.6770.1861280.19225960.19127250.9760.97699.96330.159
1.677-1.7310.2021470.18125430.18226900.970.9791000.149
1.731-1.7920.2171180.17724510.17925690.9710.9791000.145
1.792-1.8590.1581160.16423850.16325010.9840.9831000.13
1.859-1.9340.191190.15622810.15724000.9760.9841000.128
1.934-2.020.1931140.15822040.1623180.9810.9851000.13
2.02-2.1170.1751230.14420990.14622220.9820.9871000.118
2.117-2.2310.145940.12320330.12421270.9870.9911000.102
2.231-2.3650.138810.12919210.12920030.990.9999.95010.109
2.365-2.5260.176890.12918200.13119090.9830.991000.109
2.526-2.7260.171890.13717020.13917910.9820.9881000.115
2.726-2.9830.151740.14315700.14416450.9840.98799.93920.122
2.983-3.3280.16720.15214270.15214990.9860.9861000.133
3.328-3.830.186640.14912910.15113550.9810.9861000.135
3.83-4.660.161700.14410980.14511680.9830.9871000.134
4.66-6.4660.243640.1888800.1929440.9760.9811000.172
6.466-23.5960.204220.2065940.2066170.9820.97199.83790.188

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