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- PDB-7dqp: Thermal treated Marsupenaeus japonicus ferritin -

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Basic information

Entry
Database: PDB / ID: 7dqp
TitleThermal treated Marsupenaeus japonicus ferritin
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / iron / catalysis / nanocage
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol
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 speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsTan, X. / Liu, Y. / Zang, J. / Zhang, T. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Hyperthermostability of prawn ferritin nanocage facilitates its application as a robust nanovehicle for nutraceuticals.
Authors: Tan, X. / Liu, Y. / Zang, J. / Zhang, T. / Zhao, G.
History
DepositionDec 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ferritin
F: Ferritin
A: Ferritin
B: Ferritin
D: Ferritin
E: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
O: Ferritin
P: Ferritin
Q: Ferritin
R: Ferritin
S: Ferritin
T: Ferritin
U: Ferritin
V: Ferritin
W: Ferritin
X: Ferritin


Theoretical massNumber of molelcules
Total (without water)464,63124
Polymers464,63124
Non-polymers00
Water12,665703
1
C: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
S: Ferritin
T: Ferritin

A: Ferritin
B: Ferritin
D: Ferritin
E: Ferritin

O: Ferritin
P: Ferritin
Q: Ferritin
R: Ferritin

U: Ferritin
V: Ferritin

W: Ferritin
X: Ferritin

I: Ferritin
J: Ferritin


Theoretical massNumber of molelcules
Total (without water)464,63124
Polymers464,63124
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_665x+1,y+1,z1
Buried area89500 Å2
ΔGint-293 kcal/mol
Surface area130970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.624, 124.601, 124.886
Angle α, β, γ (deg.)90.420, 119.790, 119.670
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
Ferritin


Mass: 19359.635 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: T2B7E1, ferroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES-NaOH (pH 6.0), 1.26 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 259513 / % possible obs: 98.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.53 Å2 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.108 / Rrim(I) all: 0.202 / Χ2: 1.109 / Net I/σ(I): 5.8 / Num. measured all: 888983
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.20.353128280.8060.2310.4240.63997.2
2.24-2.283.10.324128450.8210.2170.3920.66697.5
2.28-2.323.30.312129610.8410.2050.3750.70397.7
2.32-2.373.50.29128840.8830.1820.3430.71697.7
2.37-2.423.50.283129650.8830.1760.3350.7197.8
2.42-2.483.60.279129300.8920.1720.3290.73997.8
2.48-2.543.50.257129330.9030.160.3030.78498
2.54-2.613.50.231129360.9040.1460.2750.82998.1
2.61-2.693.40.217129900.9120.1380.2590.88298.1
2.69-2.773.20.199129720.9080.1320.240.89698.3
2.77-2.873.40.197129850.8990.1280.2361.05998.3
2.87-2.993.60.185129590.9310.1140.2181.0998.4
2.99-3.123.60.175130590.9330.1080.2061.20198.6
3.12-3.293.60.164130280.9380.1020.1941.28198.6
3.29-3.493.40.155130160.9360.0980.1851.48698.7
3.49-3.763.30.147130730.9240.0980.1781.6398.6
3.76-4.143.60.144130670.9510.0880.171.70398.9
4.14-4.743.50.141129910.9480.0880.1671.70198.6
4.74-5.973.30.135130560.9520.0890.1621.6398.8
5.97-503.40.136130350.9570.0860.1611.70998.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4U

6a4u


Resolution: 2.203→40.62 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 16.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1795 1961 0.76 %
Rwork0.1734 257533 -
obs0.1735 259494 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.81 Å2 / Biso mean: 23.3093 Å2 / Biso min: 7.87 Å2
Refinement stepCycle: final / Resolution: 2.203→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32616 0 0 703 33319
Biso mean---22.98 -
Num. residues----4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733194
X-RAY DIFFRACTIONf_angle_d0.83444667
X-RAY DIFFRACTIONf_chiral_restr0.0424704
X-RAY DIFFRACTIONf_plane_restr0.0055929
X-RAY DIFFRACTIONf_dihedral_angle_d23.09212625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.203-2.25810.1798990.18181315569
2.2581-2.31910.21271440.16921866998
2.3191-2.38730.19311090.17381866398
2.3873-2.46440.19121600.18341872598
2.4644-2.55250.261370.18921882398
2.5525-2.65460.22041680.18131869598
2.6546-2.77540.24291370.18811881298
2.7754-2.92170.1911770.1861872498
2.9217-3.10470.2091440.19161881999
3.1047-3.34430.18071200.19441887399
3.3443-3.68070.15271450.17391897699
3.6807-4.21280.15311490.15271875699
4.2128-5.30580.13721530.14941888299
5.3058-40.620.16171190.16691896199

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