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- PDB-8i8u: Crystal structure of horse spleen L-ferritin S118A mutant at -180... -

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Basic information

Entry
Database: PDB / ID: 8i8u
TitleCrystal structure of horse spleen L-ferritin S118A mutant at -180deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / S118A mutant / X-ray structure
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
DepositionFeb 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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.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)20,81612
Polymers19,8561
Non-polymers95911
Water4,216234
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)499,582288
Polymers476,55424
Non-polymers23,028264
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 area120820 Å2
ΔGint-791 kcal/mol
Surface area137410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.296, 181.296, 181.296
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-207-

CD

21X-208-

CD

31X-209-

CD

41X-516-

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: 19856.428 Da / Num. of mol.: 1 / Mutation: S118A
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, 245 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-SO4 / SULFATE ION


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


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#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.: 234 / 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: 3.13 Å3/Da / Density % sol: 60.65 %
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: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→18.51 Å / Num. obs: 34030 / % possible obs: 99.7 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.119 / Net I/σ(I): 10.8
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1652 / CC1/2: 0.467 / Rrim(I) all: 1.272

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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→18.51 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.752 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2033 1724 5.07 %
Rwork0.171 32282 -
all0.173 --
obs-34006 99.505 %
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: 13.249 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 32 234 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121507
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161429
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.6492040
X-RAY DIFFRACTIONr_angle_other_deg0.5561.5793289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7635193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.074513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15810275
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.3991083
X-RAY DIFFRACTIONr_chiral_restr0.0820.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021810
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined0.2410.2339
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.21205
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2719
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.2812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2162
X-RAY DIFFRACTIONr_metal_ion_refined0.3360.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3790.228
X-RAY DIFFRACTIONr_nbd_other0.1670.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.237
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3720.28
X-RAY DIFFRACTIONr_mcbond_it1.7921.221715
X-RAY DIFFRACTIONr_mcbond_other1.7421.222715
X-RAY DIFFRACTIONr_mcangle_it2.8992.179897
X-RAY DIFFRACTIONr_mcangle_other2.8972.187898
X-RAY DIFFRACTIONr_scbond_it2.7561.535792
X-RAY DIFFRACTIONr_scbond_other2.7311.515781
X-RAY DIFFRACTIONr_scangle_it4.4512.6541133
X-RAY DIFFRACTIONr_scangle_other4.4292.6141116
X-RAY DIFFRACTIONr_lrange_it6.62215.5551855
X-RAY DIFFRACTIONr_lrange_other6.41613.7121770
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
1.6-1.6410.2871260.29423050.29424420.9430.93399.54960.284
1.641-1.6860.281060.27222610.27323900.9450.94599.03770.258
1.686-1.7350.2991240.25521910.25723260.9330.95199.52710.239
1.735-1.7870.2611180.23921460.2422690.9560.95799.77960.217
1.787-1.8450.2451150.22320860.22422080.960.96699.6830.197
1.845-1.910.191080.20320080.20221280.9750.97399.43610.175
1.91-1.9810.252940.18819480.19120660.9590.97798.83830.159
1.981-2.0610.185880.17518820.17619840.980.9899.29430.143
2.061-2.1510.219960.14918210.15219270.9730.98699.48110.123
2.151-2.2550.1651070.13717320.13918420.9820.98899.83710.111
2.255-2.3750.159910.13416640.13517550.9840.9881000.109
2.375-2.5160.217840.13615980.1416820.9710.9881000.111
2.516-2.6860.161700.13714980.13815680.9840.9881000.113
2.686-2.8960.19700.13714000.13914700.9790.9881000.113
2.896-3.1650.198660.14113060.14413720.9730.9871000.119
3.165-3.5260.176760.16711850.16712610.980.9841000.149
3.526-4.0470.178760.1410500.14311260.9790.9881000.128
4.047-4.8980.151490.1299280.139780.9870.98999.89780.118
4.898-6.6970.244430.2027540.2047970.9720.981000.178
6.697-18.510.281170.1885190.1915440.9630.97698.52940.172

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