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- PDB-7usn: Crystal structure of ferritin 1 from Caenorhabditis elegans, FTN-1 -

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Basic information

Entry
Database: PDB / ID: 7usn
TitleCrystal structure of ferritin 1 from Caenorhabditis elegans, FTN-1
ComponentsFerritin
KeywordsOXIDOREDUCTASE / Ferroxidase
Function / homology
Function and homology information


Iron uptake and transport / : / Neutrophil degranulation / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / identical protein binding / cytoplasm
Similarity search - Function
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
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.789 Å
AuthorsMalcolm, T.R. / Maher, M.J. / Mubarak, S.S.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Biochemistry / Year: 2023
Title: Biochemical Characterization of Caenorhabditis elegans Ferritins.
Authors: Mubarak, S.S.M. / Malcolm, T.R. / Brown, H.G. / Hanssen, E. / Maher, M.J. / McColl, G. / Jameson, G.N.L.
History
DepositionApr 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
O: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
P: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,83371
Polymers309,28816
Non-polymers4,54555
Water43,2902403
1
A: Ferritin
C: Ferritin
D: Ferritin
F: Ferritin
O: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
D: Ferritin
F: Ferritin
O: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
D: Ferritin
F: Ferritin
O: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,182111
Polymers463,93324
Non-polymers7,24987
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area112190 Å2
ΔGint-827 kcal/mol
Surface area131550 Å2
MethodPISA
2
B: Ferritin
E: Ferritin
G: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
P: Ferritin
hetero molecules

B: Ferritin
E: Ferritin
G: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
P: Ferritin
hetero molecules

B: Ferritin
E: Ferritin
G: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
P: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,317102
Polymers463,93324
Non-polymers6,38578
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area112070 Å2
ΔGint-755 kcal/mol
Surface area130560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.763, 227.763, 227.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-382-

HOH

21A-422-

HOH

31B-362-

HOH

41B-408-

HOH

51I-2059-

HOH

61I-2073-

HOH

71L-387-

HOH

81L-422-

HOH

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Components

#1: Protein
Ferritin


Mass: 19330.527 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ftn-1, C54F6.14, CELE_C54F6.14 / Production host: Escherichia coli (E. coli) / References: UniProt: O16453, ferroxidase
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2403 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Ammonium sulfate, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.789→50 Å / Num. obs: 365928 / % possible obs: 99.9 % / Redundancy: 21.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.036 / Net I/σ(I): 12.2
Reflection shellResolution: 1.79→1.82 Å / Rmerge(I) obs: 1.567 / Num. unique obs: 17721 / CC1/2: 0.806 / Rpim(I) all: 0.347

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.789→48.559 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.176 / WRfactor Rwork: 0.158 / SU B: 1.21 / SU ML: 0.041 / Average fsc free: 0.9847 / Average fsc work: 0.9889 / Cross valid method: FREE R-VALUE / ESU R: 0.02 / ESU R Free: 0.019
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1885 17988 4.916 %
Rwork0.1657 347910 -
all0.167 --
obs-365898 99.892 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.536 Å2
Baniso -1Baniso -2Baniso -3
1--14.794 Å26.306 Å2-19.507 Å2
2---14.976 Å2-19.43 Å2
3---29.77 Å2
Refinement stepCycle: LAST / Resolution: 1.789→48.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21792 0 235 2403 24430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01322551
X-RAY DIFFRACTIONr_bond_other_d0.0010.01621002
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.63730347
X-RAY DIFFRACTIONr_angle_other_deg1.3861.58448104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59252706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55222.6271500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.889153979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.40215188
X-RAY DIFFRACTIONr_chiral_restr0.0740.22785
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025620
X-RAY DIFFRACTIONr_nbd_refined0.2060.24897
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.218656
X-RAY DIFFRACTIONr_nbtor_refined0.1640.211119
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.29971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.22038
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1060.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.2111
X-RAY DIFFRACTIONr_nbd_other0.1850.2604
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.2196
X-RAY DIFFRACTIONr_mcbond_it1.3162.44310821
X-RAY DIFFRACTIONr_mcbond_other1.3162.44310820
X-RAY DIFFRACTIONr_mcangle_it1.8183.65813528
X-RAY DIFFRACTIONr_mcangle_other1.8183.65813529
X-RAY DIFFRACTIONr_scbond_it2.4532.82411730
X-RAY DIFFRACTIONr_scbond_other2.4472.80611671
X-RAY DIFFRACTIONr_scangle_it3.7834.11316817
X-RAY DIFFRACTIONr_scangle_other3.7854.08316728
X-RAY DIFFRACTIONr_lrange_it4.98430.25926991
X-RAY DIFFRACTIONr_lrange_other4.79329.70626392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.789-1.8360.27413480.228251590.23268890.9880.99298.57930.223
1.836-1.8860.23713310.192249360.195262670.9880.9921000.186
1.886-1.9410.23212170.182242800.185254970.9860.9921000.172
1.941-20.20712740.17235970.171248720.9870.99199.9960.157
2-2.0660.19111600.161228640.163240240.9870.9911000.147
2.066-2.1380.19111320.158221350.159232670.9850.991000.143
2.138-2.2190.18811330.155213350.156224680.9840.991000.139
2.219-2.3090.1810800.153205620.155216420.9840.9891000.138
2.309-2.4110.16710020.145197760.146207780.9860.991000.129
2.411-2.5290.1749670.148189130.149198800.9840.9891000.132
2.529-2.6650.1799490.154179360.155188850.9820.9871000.138
2.665-2.8260.1778630.154170790.155179420.9830.9871000.138
2.826-3.0210.1787920.16160070.161167990.9820.9861000.147
3.021-3.2620.1877320.171150110.172157430.980.9841000.16
3.262-3.5710.1787300.168137190.169144490.9840.9851000.161
3.571-3.990.1716400.156124850.157131260.9850.98799.99240.151
3.99-4.6020.1585740.143110790.144116530.9860.9891000.141
4.602-5.6240.2074890.19193840.19298730.9830.9861000.186
5.624-7.8990.2453700.2373650.2377450.9730.97699.87090.219
7.899-48.0090.2152050.20242880.20244950.9840.98299.95550.224

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