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- PDB-6iaf: Fifteen minutes iron loaded Rana Catesbeiana H' ferritin variant H54N -

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Basic information

Entry
Database: PDB / ID: 6iaf
TitleFifteen minutes iron loaded Rana Catesbeiana H' ferritin variant H54N
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / Rana Catesbeiana H' ferritin / ferroxidase process / H54N variant / fifteen minutes iron loaded / time-controlled iron loading
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / cellular iron ion homeostasis / cell / iron ion transport
Ferritin-like diiron domain / Ferritin-like / Ferritin-like diiron domain profile. / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin-like domain / Ferritin / Ferritin/DPS protein domain / Ferritin, conserved site / Ferritin-like superfamily
Ferritin, middle subunit
Biological speciesLithobates catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPozzi, C. / Di Pisa, F. / Mangani, S.
CitationJournal: J.Inorg.Biochem. / Year: 2019
Title: Effect of the point mutation H54N on the ferroxidase process of Rana catesbeiana H' ferritin.
Authors: Pozzi, C. / Di Pisa, F. / Lalli, D. / Rosa, C. / Turano, P. / Mangani, S.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,42323
Polymers20,5991
Non-polymers82422
Water6,503361
1
A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules

A: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,162552
Polymers494,37924
Non-polymers19,783528
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_556-y,-x,-z+11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_545y,z-1/2,x+1/21
crystal symmetry operation34_545-y,z-1/2,-x+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation36_555-y,-z+1/2,x+1/21
crystal symmetry operation41_545x,z-1/2,-y+1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_555-x,-z+1/2,-y+1/21
crystal symmetry operation44_555x,-z+1/2,y+1/21
crystal symmetry operation53_455z-1/2,x,y+1/21
crystal symmetry operation54_455z-1/2,-x,-y+1/21
crystal symmetry operation55_555-z+1/2,-x,y+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation69_455z-1/2,y,-x+1/21
crystal symmetry operation70_455z-1/2,-y,x+1/21
crystal symmetry operation71_555-z+1/2,y,x+1/21
crystal symmetry operation72_555-z+1/2,-y,-x+1/21
Unit cell
γ
α
β
Length a, b, c (Å)183.720, 183.720, 183.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-59-

ARG

21A-201-

FE2

31A-205-

FE2

41A-206-

FE2

51A-208-

MG

61A-211-

MG

71A-216-

CL

81A-497-

HOH

91A-611-

HOH

101A-661-

HOH

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Components

#1: Protein/peptide Ferritin, middle subunit / / Ferritin M / Ferritin H' / Ferritin X


Mass: 20599.137 Da / Num. of mol.: 1 / Mutation: H54N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lithobates catesbeiana (American bullfrog)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P07798, ferroxidase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Iron
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Magnesium
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl / Chloride
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.26 Å3/Da / Density % sol: 62.32 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.6-2.0 M MgCl2 and 0.1 M bicine pH 9.0 / PH range: 8-9

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Data collection

Diffraction

Mean temperature: 100 K / Crystal-ID: 1 / Serial crystal experiment: N

ID
1
2
3
Diffraction source

Source: SYNCHROTRON

SiteBeamlineDiffraction-IDWavelength (Å)
ESRF BM1410.95372
ELETTRA 5.2R21.73893
ELETTRA 5.2R31.76116
Detector
TypeDiffraction-IDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 8, 2012
DECTRIS PILATUS 2M2PIXELOct 29, 2012
DECTRIS PILATUS 2M3PIXELOct 29, 2012
Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Diffraction-IDWavelength-ID
11
22
33
Radiation wavelength
IDWavelength (Å)Relative weight
10.953721
21.738931
31.761161
Reflection

Biso Wilson estimate: 9.93 Å2 / Entry-ID: 6IAF / Observed criterion σ(I): 2

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)CC1/2
1.35-22.445851210014.20.0730.0210.078122.3
1.78-45.922593399.88.90.1110.0420.129212.40.996
2.34-42.06116771009.80.180.060.1937.30.958
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allDiffraction-ID% possible allCC1/2
1.35-1.4213.80.447683880.1280.481100
1.78-1.884.60.544236370.3040.682990.767
2.34-2.4710.20.783.516560.2550.82231000.795

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LQH
Resolution: 1.35→22.44 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.958 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14072 2960 5.1 %RANDOM
Rwork0.11326 ---
Obs0.11465 55550 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.748 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.121 Å
Refinement stepCycle: 1 / Resolution: 1.35→22.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 22 361 1796
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0090.0131646
r_bond_other_d0.0010.0171513
r_angle_refined_deg1.4811.6492250
r_angle_other_deg1.5851.5923567
r_dihedral_angle_1_deg4.5475220
r_dihedral_angle_2_deg36.64423.423111
r_dihedral_angle_3_deg13.3315332
r_dihedral_angle_4_deg20.3921512
r_chiral_restr0.0810.2203
r_gen_planes_refined0.0080.021914
r_gen_planes_other0.0010.02354
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.927756
r_mcbond_other0.924755
r_mcangle_it1.133959
r_mcangle_other1.133960
r_scbond_it1.414890
r_scbond_other1.414891
r_scangle_it
r_scangle_other1.7591267
r_long_range_B_refined3.3722092
r_long_range_B_other2.0251990
r_rigid_bond_restr1.62431207
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.165 208 -
Rwork0.158 4038 -
Obs--99.98 %

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