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Basic information

Entry
Database: PDB / ID: 5jkm
TitleBinary crystal structure of positively and negatively supercharged variants Ftn(pos) and Ftn(neg) from human heavy chain ferritin (Mg acetate condition)
Components(Ferritin heavy ...) x 2
KeywordsOXIDOREDUCTASE / protein design / protein engineering / charged protein containers / binary protein structures / self-assembly / binary nanoparticle superlattices
Function / homology
Function and homology information


iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / 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, 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 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKuenzle, M. / Beck, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Binary Protein Crystals for the Assembly of Inorganic Nanoparticle Superlattices.
Authors: Kunzle, M. / Eckert, T. / Beck, T.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,39643
Polymers257,12912
Non-polymers1,26831
Water27,2931515
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,83788
Polymers515,98224
Non-polymers2,85564
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area98010 Å2
ΔGint-830 kcal/mol
Surface area144070 Å2
MethodPISA
2
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,74884
Polymers512,53324
Non-polymers2,21560
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area97250 Å2
ΔGint-880 kcal/mol
Surface area141260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.840, 126.840, 175.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

21C-424-

HOH

31F-421-

HOH

41G-411-

HOH

51I-302-

HOH

61J-383-

HOH

71L-392-

HOH

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Components

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Ferritin heavy ... , 2 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Ferritin heavy chain / / Ferritin H subunit / Cell proliferation-inducing gene 15 protein / Positively charged variant of ...Ferritin H subunit / Cell proliferation-inducing gene 15 protein / Positively charged variant of human heavy chain ferritin


Mass: 21499.246 Da / Num. of mol.: 6
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, ferroxidase
#2: Protein
Ferritin heavy chain / / Ferritin H subunit / Cell proliferation-inducing gene 15 protein / Negatively charged variant of ...Ferritin H subunit / Cell proliferation-inducing gene 15 protein / Negatively charged variant of human heavy chain ferritin


Mass: 21355.549 Da / Num. of mol.: 6
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, ferroxidase

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Non-polymers , 4 types, 1546 molecules

#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1515 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.20 M magnesium acetate, 100 mM Tris, pH 8.5, 8 mg/mL Ftn(pos) and 8 mg/mL Ftn(neg)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.6 Å / Num. obs: 253942 / % possible obs: 99.6 % / Redundancy: 5.65 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.0628 / Net I/σ(I): 19.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.16 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.71 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKL

5jkl


Resolution: 1.8→47.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.142 / SU ML: 0.067 / SU R Cruickshank DPI: 0.0976 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.098
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 12649 5 %RANDOM
Rwork0.159 ---
obs0.1606 241293 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.66 Å2 / Biso mean: 20.301 Å2 / Biso min: 9.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.8→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17124 0 41 1515 18680
Biso mean--31.62 25.77 -
Num. residues----2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01917470
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216506
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.94923458
X-RAY DIFFRACTIONr_angle_other_deg0.911338008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60252052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.50924.94996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.853153318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.20715102
X-RAY DIFFRACTIONr_chiral_restr0.1150.22450
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024212
X-RAY DIFFRACTIONr_mcbond_it1.5841.7538244
X-RAY DIFFRACTIONr_mcbond_other1.5761.7538243
X-RAY DIFFRACTIONr_mcangle_it2.042.6210284
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 962 -
Rwork0.215 17245 -
all-18207 -
obs--96.32 %

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