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- PDB-8aav: Human heavy chain ferritin with introduced Cys residues modified ... -

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Basic information

Entry
Database: PDB / ID: 8aav
TitleHuman heavy chain ferritin with introduced Cys residues modified with C10 ligand
ComponentsFerritin heavy chain, N-terminally processed
KeywordsOXIDOREDUCTASE / PROTEIN DESIGN / PROTEIN ENGINEERING / CHARGED PROTEIN CONTAINERS / SELF-ASSEMBLY / PROTEIN MODIFICATION / UREMIX TOXINS
Function / homology
Function and homology information


iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / 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
AuthorsBoehler, H. / Beck, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)401323995 Germany
German Research Foundation (DFG)413227073 Germany
CitationJournal: J Mater Chem B / Year: 2022
Title: Assembly of chemically modified protein nanocages into 3D materials for the adsorption of uremic toxins.
Authors: Bohler, H. / Orth-Alampour, S. / Baaten, C. / Riedner, M. / Jankowski, J. / Beck, T.
History
DepositionJul 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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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
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,17747
Polymers168,9148
Non-polymers5,26339
Water19,3841076
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
G: Ferritin heavy chain, N-terminally processed
H: 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
G: Ferritin heavy chain, N-terminally processed
H: 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
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,531141
Polymers506,74224
Non-polymers15,789117
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Unit cell
Length a, b, c (Å)181.440, 181.440, 181.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11B-204-

MG

21B-205-

MG

31C-205-

MG

41E-204-

MG

51F-205-

MG

61G-204-

MG

71B-411-

HOH

81E-307-

HOH

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Components

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


Mass: 21114.242 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794
#2: Chemical
ChemComp-O3K / 2-bromanyl-N-decyl-ethanamide / 2-bromo-N-decyl acetamide (C10)


Mass: 278.229 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C12H24BrNO
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1076 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystallization of little amounts of protein or functionalized protein variants were performed via hanging drop vapor diffusion techniques. Reservoir solution (100 mM Tris, 500 mM MgOAc, pH ...Details: Crystallization of little amounts of protein or functionalized protein variants were performed via hanging drop vapor diffusion techniques. Reservoir solution (100 mM Tris, 500 mM MgOAc, pH 8.5) was prepared in a 24- well manual plate set. Drops were prepared on siliconized glass cover slides (Jena Bioscience) by mixing 2 microL reservoir solutions with 1 microL 50 mM Tris, 1 M NaCl, pH 7.5 buffer and 1 microL of respective ferritin variant. Plates were incubated at 298K. After one day first crystals were visible.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→48.54 Å / Num. obs: 132696 / % possible obs: 99.9 % / Redundancy: 20.9 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.012 / Rrim(I) all: 0.054 / Net I/σ(I): 43.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0320.20.18113145564970.9950.0410.1861698.5
10.96-48.4118.60.039165988910.9990.0090.0461.399

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKK

5jkk


Resolution: 2→48.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.269 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.177 2101 1.6 %RANDOM
Rwork0.1444 ---
obs0.1449 131264 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.17 Å2 / Biso mean: 16.458 Å2 / Biso min: 5.59 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11301 0 135 1076 12512
Biso mean--34.96 24.04 -
Num. residues----1377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01311637
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610605
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.63615671
X-RAY DIFFRACTIONr_angle_other_deg1.5081.58624459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31151369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29323.936752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.787152072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8651556
X-RAY DIFFRACTIONr_chiral_restr0.0920.21409
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022713
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 153 -
Rwork0.144 9557 -
all-9710 -
obs--98.76 %

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