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- PDB-8iqy: Asterias forbesii ferritin mutant-P156H -

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Basic information

Entry
Database: PDB / ID: 8iqy
TitleAsterias 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: 2.1 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)57,8803
Polymers57,8803
Non-polymers00
Water9,242513
1
H: Ferritin
A: Ferritin
B: Ferritin
x 8


Theoretical massNumber of molelcules
Total (without water)463,04424
Polymers463,04424
Non-polymers00
Water43224
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 area85440 Å2
ΔGint-377 kcal/mol
Surface area138940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.934, 116.934, 206.539
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: 19293.488 Da / Num. of mol.: 3 / 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.: 513 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM imidazole, 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: 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: 2.1→27.56 Å / Num. obs: 42226 / % possible obs: 99.74 % / Redundancy: 13 % / Biso Wilson estimate: 23.49 Å2 / CC1/2: 0.943 / Net I/σ(I): 2.7
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 42226 / CC1/2: 0.938

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874phasing
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27.56 Å / SU ML: 0.1537 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.3277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1829 1998 4.74 %
Rwork0.1645 40172 -
obs0.1654 42170 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 0 513 4515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694077
X-RAY DIFFRACTIONf_angle_d0.78845502
X-RAY DIFFRACTIONf_chiral_restr0.0426600
X-RAY DIFFRACTIONf_plane_restr0.005714
X-RAY DIFFRACTIONf_dihedral_angle_d14.195534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.1841380.17312763X-RAY DIFFRACTION98.31
2.15-2.210.21271420.172851X-RAY DIFFRACTION99.93
2.21-2.270.19581390.17072809X-RAY DIFFRACTION99.9
2.27-2.340.21771400.17462821X-RAY DIFFRACTION99.87
2.34-2.430.21671420.16512850X-RAY DIFFRACTION99.97
2.43-2.530.17841430.16612854X-RAY DIFFRACTION100
2.53-2.640.1831410.16612846X-RAY DIFFRACTION99.97
2.64-2.780.19561420.15812853X-RAY DIFFRACTION99.93
2.78-2.950.19841420.16662870X-RAY DIFFRACTION99.97
2.95-3.180.19661430.15782869X-RAY DIFFRACTION100
3.18-3.50.1741440.1612882X-RAY DIFFRACTION100
3.5-4.010.15841460.14862918X-RAY DIFFRACTION99.93
4.01-5.040.15771450.14692932X-RAY DIFFRACTION100
5.04-27.560.18641510.19863054X-RAY DIFFRACTION99.04

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