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- PDB-8iqv: Asterias forbesii ferritin -

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Basic information

Entry
Database: PDB / ID: 8iqv
TitleAsterias forbesii ferritin
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Asterias forbesii ferritin
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesAsterias forbesi (Forbes's starfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsZhao, G. / Zhang, C. / Zang, J. / Zhang, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Foods / Year: 2023
Title: Preparation and Unique Three-Dimensional Self-Assembly Property of Starfish Ferritin.
Authors: Zhang, C. / Chen, X. / Liu, B. / Zang, J. / Zhang, T. / Zhao, G.
History
DepositionMar 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Ferritin
A: Ferritin
B: Ferritin


Theoretical massNumber of molelcules
Total (without water)58,1513
Polymers58,1513
Non-polymers00
Water00
1
H: Ferritin
A: Ferritin
B: Ferritin
x 8


Theoretical massNumber of molelcules
Total (without water)465,20824
Polymers465,20824
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area85900 Å2
ΔGint-378 kcal/mol
Surface area137910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.520, 116.520, 205.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Ferritin


Mass: 19383.650 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asterias forbesi (Forbes's starfish) / Production host: Escherichia coli (E. coli) / References: UniProt: O02384, ferroxidase

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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 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM imidazole (pH 8.0), 15%(v/v) reagent alcohol, 200 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.2915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2915 Å / Relative weight: 1
ReflectionResolution: 1.91→43.61 Å / Num. obs: 103947 / % possible obs: 99.41 % / Redundancy: 10 % / Biso Wilson estimate: 25.84 Å2 / CC1/2: 0.997 / Net I/σ(I): 6.9
Reflection shellResolution: 1.91→2.01 Å / Num. unique obs: 103947 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874phasing
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→43.61 Å / SU ML: 0.2931 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.767
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2484 3792 3.65 %
Rwork0.2193 100155 -
obs0.2203 103947 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.31 Å2
Refinement stepCycle: LAST / Resolution: 1.91→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 0 0 3993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084068
X-RAY DIFFRACTIONf_angle_d0.82675493
X-RAY DIFFRACTIONf_chiral_restr0.0481600
X-RAY DIFFRACTIONf_plane_restr0.0059714
X-RAY DIFFRACTIONf_dihedral_angle_d14.2906534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.930.40061220.3793255X-RAY DIFFRACTION87.01
1.93-1.960.39581250.373463X-RAY DIFFRACTION92.02
1.96-1.990.40931380.34323613X-RAY DIFFRACTION96.2
1.99-2.010.35371370.30623698X-RAY DIFFRACTION99.46
2.01-2.040.35731360.29973767X-RAY DIFFRACTION99.8
2.04-2.080.29081420.28593693X-RAY DIFFRACTION99.92
2.08-2.110.27211410.26343792X-RAY DIFFRACTION100
2.11-2.150.32371410.24653702X-RAY DIFFRACTION100
2.15-2.190.25671430.25473758X-RAY DIFFRACTION99.97
2.19-2.230.29741440.24563747X-RAY DIFFRACTION99.97
2.23-2.270.27261420.25223774X-RAY DIFFRACTION100
2.27-2.320.31041440.2473707X-RAY DIFFRACTION100
2.32-2.380.25581410.23843757X-RAY DIFFRACTION100
2.38-2.440.22031450.24393752X-RAY DIFFRACTION100
2.44-2.50.27011430.23843714X-RAY DIFFRACTION100
2.5-2.580.27581430.23633781X-RAY DIFFRACTION100
2.58-2.660.27671370.23233713X-RAY DIFFRACTION100
2.66-2.750.23131430.22383747X-RAY DIFFRACTION100
2.75-2.860.26961460.2383747X-RAY DIFFRACTION100
2.87-30.26671360.23063777X-RAY DIFFRACTION100
3-3.150.26661440.23213722X-RAY DIFFRACTION100
3.15-3.350.23651440.2093749X-RAY DIFFRACTION100
3.35-3.610.2541440.20513723X-RAY DIFFRACTION100
3.61-3.970.21151430.18383753X-RAY DIFFRACTION100
3.97-4.550.19861440.15343762X-RAY DIFFRACTION100
4.55-5.720.18831400.17513753X-RAY DIFFRACTION100
5.73-43.610.18081440.17373736X-RAY DIFFRACTION99.67

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