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- PDB-8ir0: AfFer mutant-P156F -

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Basic information

Entry
Database: PDB / ID: 8ir0
TitleAfFer mutant-P156F
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Asterias forbesii ferritin / mutant-P156F
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: 2.89 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)57,9083
Polymers57,9083
Non-polymers00
Water00
1
H: Ferritin
A: Ferritin
B: Ferritin
x 8


Theoretical massNumber of molelcules
Total (without water)463,26024
Polymers463,26024
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 area85820 Å2
ΔGint-381 kcal/mol
Surface area137060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.513, 116.513, 206.664
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: 19302.516 Da / Num. of mol.: 3 / Mutation: P156F
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

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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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, 20%(v/v) 1,4-butanediol, 200 mM Lithium sulfate, pH 6.0

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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: 2.89→29.65 Å / Num. obs: 16300 / % possible obs: 99.71 % / Redundancy: 12.7 % / Biso Wilson estimate: 45.11 Å2 / CC1/2: 0.972 / Net I/σ(I): 2
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.519 / Num. unique obs: 16300

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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: 2.89→29.65 Å / SU ML: 0.2952 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 1629 10.01 %
Rwork0.1852 14642 -
obs0.1902 16271 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.63 Å2
Refinement stepCycle: LAST / Resolution: 2.89→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 0 0 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01054080
X-RAY DIFFRACTIONf_angle_d1.12035505
X-RAY DIFFRACTIONf_chiral_restr0.0515600
X-RAY DIFFRACTIONf_plane_restr0.0066714
X-RAY DIFFRACTIONf_dihedral_angle_d14.4802534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.980.28441300.20381172X-RAY DIFFRACTION98.86
2.98-3.070.33471340.20551210X-RAY DIFFRACTION100
3.07-3.180.25441320.2051182X-RAY DIFFRACTION100
3.18-3.310.25581360.20411222X-RAY DIFFRACTION100
3.31-3.460.2561330.20131192X-RAY DIFFRACTION99.92
3.46-3.640.2491340.20291215X-RAY DIFFRACTION99.93
3.64-3.870.2471350.1891210X-RAY DIFFRACTION100
3.87-4.170.23121350.17261216X-RAY DIFFRACTION100
4.17-4.580.19521360.14691227X-RAY DIFFRACTION100
4.59-5.240.19651370.16191227X-RAY DIFFRACTION99.85
5.25-6.60.26341400.20931268X-RAY DIFFRACTION99.93
6.6-29.650.19761470.18291301X-RAY DIFFRACTION98.37

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