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- PDB-8iqx: ferritin mutant-P156H -

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Basic information

Entry
Database: PDB / ID: 8iqx
Titleferritin 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
H: Ferritin
J: Ferritin
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin


Theoretical massNumber of molelcules
Total (without water)155,3978
Polymers155,3978
Non-polymers00
Water9,008500
1
H: Ferritin
J: Ferritin
A: Ferritin
B: Ferritin

H: Ferritin
J: Ferritin
A: Ferritin
B: Ferritin

H: Ferritin
J: Ferritin
A: Ferritin
B: Ferritin

C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin

C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin

C: Ferritin
D: Ferritin
E: 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 operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_445-x-1/2,-y-1/2,z+1/21
crystal symmetry operation18_544z+1/2,-x-1/2,-y-1/21
crystal symmetry operation22_454-y-1/2,z+1/2,-x-1/21
Buried area85160 Å2
ΔGint-376 kcal/mol
Surface area135960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.157, 229.157, 229.157
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
11B-210-

HOH

21B-217-

HOH

31C-229-

HOH

41C-248-

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.: 500 / 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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM imidazole, 15%(v/v) reagent alcohol, 200 mM magnesium chloride, 2.0 mM nickel 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→28.64 Å / Num. obs: 1269561 / % possible obs: 99.84 % / Redundancy: 18.5 % / Biso Wilson estimate: 32.23 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 2.2
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 68784 / CC1/2: 0.929

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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→28.64 Å / SU ML: 0.3235 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2583 3898 2.91 %
Rwork0.208 130178 -
obs0.2095 134076 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10672 0 0 500 11172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008510872
X-RAY DIFFRACTIONf_angle_d0.981414672
X-RAY DIFFRACTIONf_chiral_restr0.05351600
X-RAY DIFFRACTIONf_plane_restr0.00611904
X-RAY DIFFRACTIONf_dihedral_angle_d14.51091424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.35691340.26064671X-RAY DIFFRACTION99.98
2.53-2.560.2711360.25024653X-RAY DIFFRACTION99.98
2.56-2.60.36581440.24694677X-RAY DIFFRACTION100
2.6-2.630.29021400.24724560X-RAY DIFFRACTION99.91
2.63-2.670.3181360.24474721X-RAY DIFFRACTION99.98
2.67-2.710.3221360.254644X-RAY DIFFRACTION99.9
2.71-2.750.31811460.23864651X-RAY DIFFRACTION99.98
2.75-2.80.28481420.2324679X-RAY DIFFRACTION99.98
2.8-2.840.3451320.24254594X-RAY DIFFRACTION99.98
2.85-2.90.30021460.24084675X-RAY DIFFRACTION99.98
2.9-2.950.29931420.22484684X-RAY DIFFRACTION100
2.95-3.010.28891320.21864662X-RAY DIFFRACTION99.98
3.01-3.080.27851400.23254639X-RAY DIFFRACTION99.98
3.08-3.150.25981420.22424678X-RAY DIFFRACTION100
3.15-3.230.20931400.20994620X-RAY DIFFRACTION100
3.23-3.320.28431380.20854635X-RAY DIFFRACTION100
3.32-3.410.28791440.21314672X-RAY DIFFRACTION100
3.41-3.520.29971350.20764658X-RAY DIFFRACTION100
3.52-3.650.24481360.19834670X-RAY DIFFRACTION100
3.65-3.790.24521420.18294681X-RAY DIFFRACTION100
3.8-3.970.24441480.18774652X-RAY DIFFRACTION100
3.97-4.170.24131340.18744633X-RAY DIFFRACTION100
4.18-4.430.2361420.18084632X-RAY DIFFRACTION99.96
4.44-4.780.21221420.17024673X-RAY DIFFRACTION100
4.78-5.250.19821390.194668X-RAY DIFFRACTION100
5.26-6.010.28591460.21674627X-RAY DIFFRACTION99.98
6.01-7.550.21261280.21024688X-RAY DIFFRACTION99.94
7.56-28.640.20651360.19574481X-RAY DIFFRACTION96.03

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