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- PDB-7owy: Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-l... -

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Basic information

Entry
Database: PDB / ID: 7owy
TitleCrystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 3 minutes showing a peroxide anion as bridging species of iron ions in the ferroxidase site
ComponentsFerritin, mitochondrial
KeywordsOXIDOREDUCTASE / human mitochondrial ferritin / hMTF / time-controlled iron loading / ferroxidase site / peroxide anion
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / protein maturation / iron ion transport / Iron uptake and transport / ferrous iron binding / intracellular iron ion homeostasis / iron ion binding / mitochondrial matrix ...ferroxidase / ferroxidase activity / ferric iron binding / protein maturation / iron ion transport / Iron uptake and transport / ferrous iron binding / intracellular iron ion homeostasis / iron ion binding / mitochondrial matrix / mitochondrion / nucleus / cytoplasm
Similarity search - Function
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 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
: / HYDROGEN PEROXIDE / Ferritin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPozzi, C. / Ciambellotti, S. / Tassone, G. / Turano, P. / Mangani, S.
CitationJournal: Chemistry / Year: 2021
Title: Iron Binding in the Ferroxidase Site of Human Mitochondrial Ferritin.
Authors: Ciambellotti, S. / Pratesi, A. / Tassone, G. / Turano, P. / Mangani, S. / Pozzi, C.
History
DepositionJun 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,83517
Polymers21,1081
Non-polymers72716
Water6,161342
1
A: Ferritin, mitochondrial
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)524,031408
Polymers506,58224
Non-polymers17,449384
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
Unit cell
Length a, b, c (Å)184.111, 184.111, 184.111
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-202-

FE2

21A-205-

FE2

31A-208-

FE2

41A-209-

FE2

51A-213-

CL

61A-324-

HOH

71A-490-

HOH

81A-593-

HOH

91A-607-

HOH

101A-624-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin, mitochondrial


Mass: 21107.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTMT / Plasmid: pET-3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pLysS / References: UniProt: Q8N4E7, ferroxidase

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Non-polymers , 5 types, 358 molecules

#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.16 Å3/Da / Density % sol: 61.07 % / Description: Octahedral crystals
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: 1.6-2 M MgCl2 6H2O and 0.1 M bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 7, 2018
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→65.09 Å / Num. obs: 39259 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 21.2 % / Biso Wilson estimate: 10.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.036 / Rrim(I) all: 0.168 / Net I/σ(I): 12
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 20.9 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 5609 / CC1/2: 0.929 / Rpim(I) all: 0.141 / Rrim(I) all: 0.646 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R03

1r03


Resolution: 1.55→55.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.964 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1722 1949 5 %RANDOM
Rwork0.1527 ---
obs0.1536 37229 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.22 Å2 / Biso mean: 15.044 Å2 / Biso min: 4.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.137 Å
Refinement stepCycle: final / Resolution: 1.55→55.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 17 368 1791
Biso mean--17.04 27.47 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121639
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.642239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0235215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14122.301113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94815307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2441515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021313
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 136 -
Rwork0.194 2695 -
all-2831 -
obs--99.58 %

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