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- PDB-7xrg: ferritin nanocage assembly with nickel ion -

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Basic information

Entry
Database: PDB / ID: 7xrg
Titleferritin nanocage assembly with nickel ion
ComponentsFerritin
KeywordsPROTEIN BINDING
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, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / NICKEL (II) ION / Ferritin
Similarity search - Component
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhao, G.H. / Zhang, X.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972018 China
CitationJournal: To Be Published
Title: ferritin nanocage assembly with nickel ion
Authors: Zhao, G.H. / Zhang, X.R.
History
DepositionMay 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline ..._diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8125
Polymers19,5831
Non-polymers2294
Water1,71195
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)475,488120
Polymers469,99024
Non-polymers5,49896
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_654-x+1,y,-z-11
crystal symmetry operation4_564x,-y+1,-z-11
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation6_665z+1,-x+1,-y1
crystal symmetry operation7_564-z,-x+1,y-11
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation10_665-y+1,z+1,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_654-y+1,-z,x-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_664-y+1,-x+1,-z-11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_565x,z+1,-y1
crystal symmetry operation18_664-x+1,z+1,y-11
crystal symmetry operation19_655-x+1,-z,-y1
crystal symmetry operation20_554x,-z,y-11
crystal symmetry operation21_655z+1,y,-x1
crystal symmetry operation22_664z+1,-y+1,x-11
crystal symmetry operation23_554-z,y,x-11
crystal symmetry operation24_565-z,-y+1,-x1
Buried area95710 Å2
ΔGint-943 kcal/mol
Surface area133300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.278, 117.278, 117.278
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21A-202-

NI

31A-380-

HOH

41A-384-

HOH

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Components

#1: Protein Ferritin


Mass: 19582.912 Da / Num. of mol.: 1 / Mutation: Q81E, Q88R, T158H, L160H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli (E. coli) / References: UniProt: T2B7E1, ferroxidase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 293 K / Method: evaporation / Details: hepes, sodium chloride

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→58.64 Å / Num. obs: 21291 / % possible obs: 95.12 % / Redundancy: 1 % / CC1/2: 0.992 / Net I/σ(I): 4.1
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 1833 / CC1/2: 0.992

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4U

6a4u


Resolution: 1.9→58.64 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 2000 9.39 %
Rwork0.1898 19291 -
obs0.1928 21291 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.43 Å2 / Biso mean: 29.4943 Å2 / Biso min: 12.83 Å2
Refinement stepCycle: final / Resolution: 1.9→58.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 4 95 1465
Biso mean--42.22 32.26 -
Num. residues----169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.950.31211200.24441158127883
1.95-20.24481300.21811249137988
2-2.060.23031370.21131319145693
2.06-2.120.288960.2021932102866
2.13-2.20.24111460.197514161562100
2.2-2.290.28231490.204914311580100
2.29-2.390.2661500.199314401590100
2.39-2.520.27241460.215614151561100
2.52-2.680.21761500.207714431593100
2.68-2.880.2341480.216314361584100
2.88-3.170.24721520.207514591611100
3.18-3.630.22231520.188114721624100
3.63-4.580.19121550.156614981653100
4.58-58.640.17291690.167116231792100

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