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- PDB-9bxp: Nanoparticle Crystal Structure of a Thermostabilized Mutant of an... -

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Basic information

Entry
Database: PDB / ID: 9bxp
TitleNanoparticle Crystal Structure of a Thermostabilized Mutant of an As-Isolated FtnA (Ferritin) from Pseudomonas aeruginosa
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / Bactoferritin / Ferritin / nanoparticle
Function / homology
Function and homology information


iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / iron ion binding / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsSeraj, N. / Cappelli, L. / Wahome, N. / Cinelli, P. / Fabiola, G. / Cartocci, E. / Delany, I. / Cozzi, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: In silico Self-assembling Protein Nanoparticles Optimization for Protein Antigen display
Authors: Cappelli, L. / Wahome, N. / Cinelli, P. / Giusti, F. / Seraj, N. / Cartocci, E. / Harshbarger, W. / Delany, I. / Cozzi, R.
History
DepositionMay 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin


Theoretical massNumber of molelcules
Total (without water)115,7696
Polymers115,7696
Non-polymers00
Water4,594255
1
A: Bacterioferritin
B: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin

A: Bacterioferritin
B: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin

A: Bacterioferritin
B: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin

A: Bacterioferritin
B: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin

C: Bacterioferritin
F: Bacterioferritin

C: Bacterioferritin
F: Bacterioferritin

C: Bacterioferritin
F: Bacterioferritin

C: Bacterioferritin
F: Bacterioferritin


Theoretical massNumber of molelcules
Total (without water)463,07524
Polymers463,07524
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_555x+1/2,y+1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_555-y+1/2,x+1/2,z+1/21
crystal symmetry operation8_555y+1/2,-x+1/2,z+1/21
Buried area73840 Å2
ΔGint-304 kcal/mol
Surface area130780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.413, 123.413, 173.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-224-

HOH

21D-234-

HOH

31E-234-

HOH

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Components

#1: Protein
Bacterioferritin / BFR


Mass: 19294.771 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bfr, bfrA, PA4235 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWF9, ferroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 2.8 M Ammonium Sulfate, 0.1 M Sodium Citrate pH 4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→35.59 Å / Num. obs: 51690 / % possible obs: 97.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 28.17 Å2 / CC1/2: 0.851 / Net I/σ(I): 9.6
Reflection shellResolution: 2.33→2.413 Å / Num. unique obs: 4541 / CC1/2: 0.322

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→35.59 Å / SU ML: 0.2324 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 21.7824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2169 3177 3.88 %
Rwork0.1964 78780 -
obs0.1972 51690 74.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.28 Å2
Refinement stepCycle: LAST / Resolution: 2.33→35.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 0 255 7851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00777916
X-RAY DIFFRACTIONf_angle_d0.78810759
X-RAY DIFFRACTIONf_chiral_restr0.05351174
X-RAY DIFFRACTIONf_plane_restr0.00441427
X-RAY DIFFRACTIONf_dihedral_angle_d16.58773058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.247800.22221787X-RAY DIFFRACTION38.92
2.36-2.40.219970.21212358X-RAY DIFFRACTION52.09
2.4-2.440.2662950.20872428X-RAY DIFFRACTION53.83
2.44-2.480.22591120.22062539X-RAY DIFFRACTION55.54
2.48-2.530.23361050.21662556X-RAY DIFFRACTION55.87
2.53-2.580.1992960.22532413X-RAY DIFFRACTION52.6
2.58-2.630.2121120.22512620X-RAY DIFFRACTION57.27
2.63-2.690.26041290.21913056X-RAY DIFFRACTION67.48
2.69-2.750.26741130.21463295X-RAY DIFFRACTION71.43
2.75-2.820.22651300.20843384X-RAY DIFFRACTION74.45
2.82-2.890.20151420.20533528X-RAY DIFFRACTION77.1
2.89-2.980.27211570.21623621X-RAY DIFFRACTION80.01
2.98-3.070.24361400.22093852X-RAY DIFFRACTION82.74
3.07-3.180.2641440.22643813X-RAY DIFFRACTION83.52
3.18-3.310.21241660.20733881X-RAY DIFFRACTION85.81
3.31-3.460.24181560.19674049X-RAY DIFFRACTION87.82
3.46-3.640.24761400.18154107X-RAY DIFFRACTION89.28
3.64-3.870.19441820.18084173X-RAY DIFFRACTION90.92
3.87-4.170.17811740.16974167X-RAY DIFFRACTION91.64
4.17-4.590.1991600.16084204X-RAY DIFFRACTION91.6
4.59-5.250.20511580.19054090X-RAY DIFFRACTION89.98
5.25-6.610.20122010.23864422X-RAY DIFFRACTION96.74
6.61-35.590.19771880.17824437X-RAY DIFFRACTION96.7

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