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- PDB-7o64: Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-l... -

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Basic information

Entry
Database: PDB / ID: 7o64
TitleCrystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 1 minute.
ComponentsFerritin, mitochondrial
KeywordsOXIDOREDUCTASE / human mitochondrial ferritin / hMTF / time-controlled iron loading / ferroxidase site
Function / homology
Function and homology information


positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / : / ferroxidase / ferroxidase activity / ferric iron binding / Iron uptake and transport / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis ...positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / : / ferroxidase / ferroxidase activity / ferric iron binding / Iron uptake and transport / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / mitochondrial matrix / iron ion binding / positive regulation of cell population proliferation / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 1.1Nov 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)21,2795
Polymers21,1081
Non-polymers1714
Water5,098283
1
A: Ferritin, mitochondrial
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)510,696120
Polymers506,58224
Non-polymers4,11596
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_565-z,-y+1,-x1
crystal symmetry operation29_554z,x+1/2,y-1/21
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation31_554-z,-x+1/2,y-1/21
crystal symmetry operation32_555-z,x+1/2,-y+1/21
crystal symmetry operation41_555x,z+1/2,-y+1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_555-x,-z+1/2,-y+1/21
crystal symmetry operation44_554x,-z+1/2,y-1/21
crystal symmetry operation81_455y-1/2,z+1/2,x1
crystal symmetry operation82_555-y+1/2,z+1/2,-x1
crystal symmetry operation83_455y-1/2,-z+1/2,-x1
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
crystal symmetry operation85_455y-1/2,x+1/2,-z1
crystal symmetry operation86_555-y+1/2,-x+1/2,-z1
crystal symmetry operation87_455y-1/2,-x+1/2,z1
crystal symmetry operation88_555-y+1/2,x+1/2,z1
Buried area93090 Å2
ΔGint-762 kcal/mol
Surface area143400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.168, 184.168, 184.168
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-203-

CL

31A-204-

MG

41A-330-

HOH

51A-549-

HOH

61A-559-

HOH

71A-574-

HOH

81A-575-

HOH

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Components

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.2 Å3/Da / Density % sol: 61.53 % / 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 I0310.97622
SYNCHROTRONDiamond I0321.7394
SYNCHROTRONDiamond I0331.7438
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELFeb 19, 2018
DECTRIS PILATUS3 6M2PIXELFeb 19, 2018
DECTRIS PILATUS3 6M3PIXELFeb 19, 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
10.976221
21.73941
31.74381
Reflection

Biso Wilson estimate: 20.2 Å2 / Entry-ID: 7O64 / Observed criterion σ(I): 2

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.96-65.111741987.7210.9970.1660.0370.172111.3
2.7-65.26787310019.60.9640.2920.0690.30727.7
2.85-65.31675610019.60.9670.3750.0870.3935.8
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID
1.96-2.0721.50.6723.428290.9490.1490.6961
2.7-2.85190.6843.411010.9320.1630.7152
2.85-320.10.6112.99360.950.140.6353

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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: 1.96→55.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.927 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 803 4.6 %RANDOM
Rwork0.1628 ---
obs0.1647 16533 87.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.36 Å2 / Biso mean: 28.453 Å2 / Biso min: 15.54 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.1882 Å
Refinement stepCycle: final / Resolution: 1.96→55.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 4 283 1694
Biso mean--30.45 39.59 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121484
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6312013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19423.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57515268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0411510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021164
LS refinement shellResolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 64 -
Rwork0.216 1359 -
all-1423 -
obs--98.89 %

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