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- PDB-8i6l: Crystal structure of horse spleen L-ferritin at -180deg Celsius. -

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Basic information

Entry
Database: PDB / ID: 8i6l
TitleCrystal structure of horse spleen L-ferritin at -180deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / -180deg Celsius
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / 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 / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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: 1.5 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
DepositionJan 28, 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

Downloads & links

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,55219
Polymers19,8721
Non-polymers1,68018
Water4,666259
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)517,250456
Polymers476,93824
Non-polymers40,312432
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 area106380 Å2
ΔGint-1318 kcal/mol
Surface area145150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.058, 182.058, 182.058
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-605-

CD

21A-606-

CD

31A-607-

CD

41A-931-

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: 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, 277 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.: 9 / 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.: 259 / 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: 3.18 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: 1.542 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.5→18.581 Å / Num. obs: 41630 / % possible obs: 99.6 % / Redundancy: 10 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.8
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1995 / CC1/2: 0.946

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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
Starting model: 1DAT

1dat


Resolution: 1.5→18.581 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.873 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions.
RfactorNum. reflection% reflection
Rfree0.1743 2069 4.978 %
Rwork0.1549 39495 -
all0.156 --
obs-41564 99.383 %
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: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 46 259 1698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121543
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161483
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.6472095
X-RAY DIFFRACTIONr_angle_other_deg0.6111.5783420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6845203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.491513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62810287
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.0271082
X-RAY DIFFRACTIONr_chiral_restr0.0890.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021841
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
X-RAY DIFFRACTIONr_nbd_refined0.2470.2333
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.21191
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2730
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.2805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2160
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1930.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4090.225
X-RAY DIFFRACTIONr_nbd_other0.1470.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.240
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2270.24
X-RAY DIFFRACTIONr_mcbond_it1.3960.962725
X-RAY DIFFRACTIONr_mcbond_other1.3960.961725
X-RAY DIFFRACTIONr_mcangle_it2.1571.72912
X-RAY DIFFRACTIONr_mcangle_other2.1581.726913
X-RAY DIFFRACTIONr_scbond_it2.6161.25818
X-RAY DIFFRACTIONr_scbond_other2.5481.233803
X-RAY DIFFRACTIONr_scangle_it4.0352.151168
X-RAY DIFFRACTIONr_scangle_other3.9962.1161145
X-RAY DIFFRACTIONr_lrange_it5.90713.8011887
X-RAY DIFFRACTIONr_lrange_other5.57211.4661782
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
1.5-1.5390.2161390.18528060.18630050.970.97998.00330.161
1.539-1.5810.191510.18127150.18129280.9780.97997.88250.155
1.581-1.6260.1971450.1726940.17128740.9780.98298.78220.143
1.626-1.6760.1921570.16526090.16727700.9760.98399.85560.137
1.676-1.730.1761320.16625690.16627020.9820.98399.9630.138
1.73-1.790.1571310.15524680.15525990.9830.9851000.128
1.79-1.8570.1551440.15424060.15425530.9850.98699.88250.125
1.857-1.9320.1891200.15422980.15624220.9790.98699.83480.128
1.932-2.0170.1671190.15422350.15523580.9810.98699.83040.128
2.017-2.1140.148930.14321590.14322530.9870.98899.95560.122
2.114-2.2270.147990.13620530.13621570.9880.98999.76820.117
2.227-2.360.164920.13119350.13320300.9840.9999.85220.117
2.36-2.520.181980.13718340.13919400.9780.98899.58760.122
2.52-2.7180.16770.14217240.14318050.9850.98799.77840.128
2.718-2.9710.139930.14215770.14216780.9870.98799.52320.13
2.971-3.3110.181750.15614540.15715320.980.98599.80420.148
3.311-3.8030.168650.15613020.15713700.9820.98599.7810.151
3.803-4.610.168600.14911290.1511930.9830.98799.66470.151
4.61-6.3280.218390.1819200.1829610.9690.98499.79190.181
6.328-18.5810.248400.2166080.2186520.9640.97199.38650.222

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