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- PDB-7o68: Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-l... -

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Basic information

Entry
Database: PDB / ID: 7o68
TitleCrystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 120 minutes showing either a dioxygen or a superoxide anion coordinated to iron ions in the ferroxidase site.
ComponentsFerritin, mitochondrial
KeywordsOXIDOREDUCTASE / human mitochondrial ferritin / hMTF / time-controlled iron loading / ferroxidase site / dioxygen / superoxide 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
: / OXYGEN MOLECULE / Ferritin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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
DepositionApr 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,92018
Polymers21,1081
Non-polymers81217
Water5,585310
1
A: Ferritin, mitochondrial
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)526,079432
Polymers506,58224
Non-polymers19,498408
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 area106480 Å2
ΔGint-1132 kcal/mol
Surface area140330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.787, 183.787, 183.787
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-201-

FE2

21A-204-

FE2

31A-209-

FE2

41A-210-

FE2

51A-211-

FE2

61A-213-

CL

71A-326-

HOH

81A-491-

HOH

91A-568-

HOH

101A-594-

HOH

111A-597-

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, 327 molecules

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


Mass: 55.845 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.18 Å3/Da / Density % sol: 61.29 % / 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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0410.9795
SYNCHROTRONDiamond I0421.7384
SYNCHROTRONDiamond I0431.7512
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELSep 7, 2018
DECTRIS PILATUS 6M-F2PIXELSep 7, 2018
DECTRIS PILATUS 6M-F3PIXELSep 7, 2018
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)MADMx-ray2
3Si(111)MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.73841
31.75121
Reflection

Entry-ID: 7O68 / Observed criterion σ(F): 2 / % possible obs: 100 %

Resolution (Å)Num. obsRedundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.68-64.983085221.312.30.9980.1140.0260.119117.9
2.05-106.311735812.15.40.9890.2240.0690.24328.2
2.05-106.391739511.86.20.9890.2140.0660.22938.1
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID
1.68-1.7721.40.7114.544060.9340.1590.7411
2.06-2.1611.60.9022.824420.7590.2830.9732
2.05-2.1610.50.8052.824520.7680.2660.8723

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R03

1r03


Resolution: 1.68→64.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.374 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1831 1558 5.1 %RANDOM
Rwork0.1575 ---
obs0.1587 29280 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.58 Å2 / Biso mean: 18.016 Å2 / Biso min: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.1505 Å
Refinement stepCycle: final / Resolution: 1.68→64.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 18 324 1749
Biso mean--23.63 29.8 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121631
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6382230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54722.679112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81215304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6761514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021328
LS refinement shellResolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 110 -
Rwork0.223 2099 -
all-2209 -
obs--99.91 %

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