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- PDB-8iqw: AfFer(Asterias forbesii ferritin) mutant-P156H -

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Basic information

Entry
Database: PDB / ID: 8iqw
TitleAfFer(Asterias forbesii ferritin) mutant-P156H
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Asterias forbesii ferritin / mutant-P156H
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: 2.5 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
E: Ferritin
H: Ferritin
J: Ferritin
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
F: Ferritin


Theoretical massNumber of molelcules
Total (without water)155,3978
Polymers155,3978
Non-polymers00
Water8,143452
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin

E: Ferritin
H: Ferritin
J: Ferritin
F: Ferritin

E: Ferritin
H: Ferritin
J: Ferritin
F: Ferritin

E: Ferritin
H: Ferritin
J: Ferritin
F: Ferritin


Theoretical massNumber of molelcules
Total (without water)466,19224
Polymers466,19224
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation16_545x+1/2,-y-1/2,-z+1/21
crystal symmetry operation19_545-z+1/2,-x-1/2,y+1/21
crystal symmetry operation21_545y+1/2,z-1/2,x+1/21
Buried area85520 Å2
ΔGint-383 kcal/mol
Surface area135150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.469, 228.469, 228.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11J-256-

HOH

21B-215-

HOH

31B-250-

HOH

41B-268-

HOH

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Components

#1: Protein
Ferritin


Mass: 19424.682 Da / Num. of mol.: 8 / Mutation: P156H
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM imidazole, 35% MPD, 200 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 67917 / % possible obs: 99.88 % / Redundancy: 18.2 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 1.2
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.568 / Num. unique obs: 67917

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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: 2.5→30 Å / SU ML: 0.3643 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.8942
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2912 1994 2.94 %
Rwork0.2301 65848 -
obs0.2318 67842 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10672 0 0 452 11124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008110872
X-RAY DIFFRACTIONf_angle_d1.048514672
X-RAY DIFFRACTIONf_chiral_restr0.05431600
X-RAY DIFFRACTIONf_plane_restr0.00571904
X-RAY DIFFRACTIONf_dihedral_angle_d14.61381424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.30981420.25024663X-RAY DIFFRACTION100
2.57-2.630.32211390.24064651X-RAY DIFFRACTION100
2.64-2.710.32971410.25524716X-RAY DIFFRACTION100
2.71-2.80.32431400.24814652X-RAY DIFFRACTION100
2.8-2.90.36861430.264703X-RAY DIFFRACTION100
2.9-3.020.30981420.24174672X-RAY DIFFRACTION100
3.02-3.150.34931450.25464680X-RAY DIFFRACTION100
3.15-3.320.32281430.23724694X-RAY DIFFRACTION100
3.32-3.530.28621440.2334709X-RAY DIFFRACTION100
3.53-3.80.28591430.2144714X-RAY DIFFRACTION100
3.8-4.180.25141430.21144696X-RAY DIFFRACTION100
4.18-4.780.23861430.20314743X-RAY DIFFRACTION100
4.78-6.020.28591460.23344765X-RAY DIFFRACTION99.98
6.02-300.25691400.22014790X-RAY DIFFRACTION98.52

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