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- PDB-8pp5: Unitary crystal structure of positively supercharged ferritin var... -

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Basic information

Entry
Database: PDB / ID: 8pp5
TitleUnitary crystal structure of positively supercharged ferritin variant Ftn(pos)-m1 (Mg Formate condition)
ComponentsFerritin heavy chain, N-terminally processed
KeywordsOXIDOREDUCTASE / protein design / protein engineering / protein interfaces / superlattice / nanocage / ferritin / protein container / charged nanocage
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / Iron uptake and transport / iron ion transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / 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 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLang, L. / Beck, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)2056 Germany
CitationJournal: Biomacromolecules / Year: 2024
Title: Assembly Requirements for the Construction of Large-Scale Binary Protein Structures.
Authors: Lang, L. / Bohler, H. / Wagler, H. / Beck, T.
History
DepositionJul 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,24416
Polymers121,8126
Non-polymers43210
Water16,502916
1
A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
hetero molecules

A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
hetero molecules

A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
hetero molecules

A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,97864
Polymers487,24924
Non-polymers1,72940
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area94440 Å2
ΔGint-663 kcal/mol
Surface area146750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.898, 126.898, 187.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

21C-423-

HOH

31D-419-

HOH

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Components

#1: Protein
Ferritin heavy chain, N-terminally processed


Mass: 20302.033 Da / Num. of mol.: 6
Mutation: C90K, N98R, C102K, H105K N25R, N109K, D123K, E162R
Source method: isolated from a genetically manipulated source
Details: Ftn-pos-m1, positively charged human heavy chain ferritin with one crystal contact mutation reverted.
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Plasmid: pET-22b(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold / References: UniProt: P02794
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / Source method: isolated from a natural source / Formula: H2O
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: 60.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: reservoir: 0.19M Magnesium Formate Ftn(pos)-m1: 4 mg/mL in 50mM Tris pH 7.5 0.9 M NaCl 2microliter reservoir + 1microliter Ftn(pos)-m1 +1 microliterL 50mM Tris pH 7.5 0.3 M NaCl
Temp details: held constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→105.09 Å / Num. obs: 145913 / % possible obs: 98.9 % / Redundancy: 10.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.082 / Rrim(I) all: 0.193 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.61-105.0911.10.0589320.9970.0270.064
1.75-1.786.43.67165570.1842.244.335

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata scaling
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→105.086 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.156 / SU B: 3.105 / SU ML: 0.084 / Average fsc free: 0.9755 / Average fsc work: 0.9841 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1925 4906 4.926 %
Rwork0.1603 94696 -
all0.162 --
obs-99602 99.991 %
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: 26.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.545 Å2-0 Å20 Å2
2--0.545 Å2-0 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2→105.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8568 0 10 916 9494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0128746
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168286
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.6611733
X-RAY DIFFRACTIONr_angle_other_deg0.5141.59419096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60551028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.773560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.558101694
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.11710481
X-RAY DIFFRACTIONr_chiral_restr0.0760.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022072
X-RAY DIFFRACTIONr_nbd_refined0.2290.21838
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.27001
X-RAY DIFFRACTIONr_nbtor_refined0.1850.24238
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.24652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2724
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1820.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.219
X-RAY DIFFRACTIONr_nbd_other0.1780.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.267
X-RAY DIFFRACTIONr_mcbond_it2.392.5414127
X-RAY DIFFRACTIONr_mcbond_other2.3832.5414126
X-RAY DIFFRACTIONr_mcangle_it3.3664.5565150
X-RAY DIFFRACTIONr_mcangle_other3.3664.5565151
X-RAY DIFFRACTIONr_scbond_it4.1653.0414619
X-RAY DIFFRACTIONr_scbond_other4.1653.0414620
X-RAY DIFFRACTIONr_scangle_it6.4645.3326583
X-RAY DIFFRACTIONr_scangle_other6.4635.3326584
X-RAY DIFFRACTIONr_lrange_it7.41227.91110463
X-RAY DIFFRACTIONr_lrange_other7.37126.9610178
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
2-2.0520.2534100.22169600.22273710.9580.96999.98640.216
2.052-2.1080.2433210.19368150.19571360.9640.9761000.185
2.108-2.1690.2123540.17666180.17869720.9690.9811000.166
2.169-2.2360.2113150.16865010.1768160.9730.9831000.157
2.236-2.3090.1983430.16261820.16465250.9760.9841000.15
2.309-2.390.2063180.15760030.1663220.9750.98699.98420.144
2.39-2.480.212530.15958700.16161230.9750.9861000.144
2.48-2.5820.1982750.14656190.14958940.9780.9881000.134
2.582-2.6960.1992530.14754470.14957000.9780.9881000.135
2.696-2.8280.1982420.14851570.1553990.9760.9881000.137
2.828-2.9810.182310.1548970.15251280.9820.9871000.142
2.981-3.1610.1932630.15946270.16148900.9810.9871000.153
3.161-3.3790.1922230.17143240.17245470.9780.9851000.165
3.379-3.650.1911960.1740740.17142700.9810.9871000.167
3.65-3.9980.1782690.15436550.15639240.9830.9891000.153
3.998-4.4690.151890.12833820.12935710.9860.9911000.13
4.469-5.1590.1571450.12930030.1331480.9890.9931000.134
5.159-6.3140.2341590.18324870.18626470.9790.98799.96220.185
6.314-8.9140.185890.1619710.16120610.9860.98899.95150.169
8.914-105.0860.188580.21611040.21411670.980.9699.57150.249

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