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- PDB-9nht: Crystal structure of structure of WT BfrB from Pseudomonas aerugi... -

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Basic information

Entry
Database: PDB / ID: 9nht
TitleCrystal structure of structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor KM-5-35
ComponentsFerroxidase
KeywordsOXIDOREDUCTASE / biofilms / electron transport / iron storage / iron binding / iron mobilization / protein-protein interaction inhibitor
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / 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
: / PROTOPORPHYRIN IX CONTAINING FE / : / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLovell, S. / Seibold, S. / Battaile, K.P. / Yao, H. / Rivera, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10 OD030394 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI169344 United States
CitationJournal: Acs Infect Dis. / Year: 2025
Title: Inhibitors of the Bacterioferritin Ferredoxin Complex Dysregulate Iron Homeostasis and Kill Acinetobacter baumannii and Biofilm-Embedded Pseudomonas aeruginosa Cells.
Authors: Behm, A.M. / Yao, H. / Eze, E.C. / Alli, S.A. / Baugh, S.D.P. / Ametsetor, E. / Powell, K.M. / Battaile, K.P. / Seibold, S. / Lovell, S. / Bunce, R.A. / Reitz, A.B. / Rivera, M.
History
DepositionFeb 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,43869
Polymers222,96212
Non-polymers11,47657
Water20,4291134
1
A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules

A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,877138
Polymers445,92424
Non-polymers22,953114
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area96000 Å2
ΔGint-737 kcal/mol
Surface area126950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.970, 194.956, 203.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11H-201-

HEM

21H-201-

HEM

31L-201-

HEM

41L-201-

HEM

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Ferroxidase


Mass: 18580.168 Da / Num. of mol.: 12 / Fragment: BFRB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: bfrB, PA3531 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY79, ferroxidase

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Non-polymers , 6 types, 1191 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-A1BYC / 4-{[(5-bromo-2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione


Mass: 347.163 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C15H11BrN2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% v/v PEG200, 100 mM sodium acetate, pH 4.5, 100 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 30, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→48.74 Å / Num. obs: 218546 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.042 / Rrim(I) all: 0.155 / Χ2: 1.01 / Net I/σ(I): 13.3 / Num. measured all: 3021813
Reflection shellResolution: 1.85→1.88 Å / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 1.899 / Num. measured all: 143077 / Num. unique obs: 10731 / CC1/2: 0.661 / Rpim(I) all: 0.538 / Rrim(I) all: 1.974 / Χ2: 1.01 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(dev_5421: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→24.13 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1847 10998 5.04 %
Rwork0.1575 --
obs0.1589 218334 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→24.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15317 0 739 1134 17190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916488
X-RAY DIFFRACTIONf_angle_d0.90222293
X-RAY DIFFRACTIONf_dihedral_angle_d16.0166198
X-RAY DIFFRACTIONf_chiral_restr0.0462349
X-RAY DIFFRACTIONf_plane_restr0.0082803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.29653950.27016781X-RAY DIFFRACTION100
1.87-1.890.28553720.25756906X-RAY DIFFRACTION100
1.89-1.920.28053810.24896840X-RAY DIFFRACTION100
1.92-1.940.29443430.23546858X-RAY DIFFRACTION100
1.94-1.970.22763560.20796862X-RAY DIFFRACTION100
1.97-1.990.23463690.19326857X-RAY DIFFRACTION100
1.99-2.020.24243390.18926907X-RAY DIFFRACTION100
2.02-2.050.20423340.17386898X-RAY DIFFRACTION100
2.05-2.080.18813550.16326888X-RAY DIFFRACTION100
2.08-2.120.19343470.15396904X-RAY DIFFRACTION100
2.12-2.150.19113620.14646854X-RAY DIFFRACTION100
2.15-2.190.17073950.1426827X-RAY DIFFRACTION100
2.19-2.240.16773720.13846893X-RAY DIFFRACTION100
2.24-2.280.16753410.13626900X-RAY DIFFRACTION100
2.28-2.330.16163810.13176863X-RAY DIFFRACTION100
2.33-2.380.18213420.13426914X-RAY DIFFRACTION100
2.38-2.440.16243990.13016909X-RAY DIFFRACTION100
2.44-2.510.16783940.12986816X-RAY DIFFRACTION100
2.51-2.580.17183600.1336908X-RAY DIFFRACTION100
2.58-2.670.19063350.13616943X-RAY DIFFRACTION100
2.67-2.760.19553600.14496925X-RAY DIFFRACTION100
2.76-2.870.17873700.14366920X-RAY DIFFRACTION100
2.87-30.16493640.1526915X-RAY DIFFRACTION100
3-3.160.18663880.16466913X-RAY DIFFRACTION100
3.16-3.360.18983470.16926974X-RAY DIFFRACTION100
3.36-3.620.17783690.15676941X-RAY DIFFRACTION100
3.62-3.980.184250.15046922X-RAY DIFFRACTION100
3.98-4.550.14533660.12326990X-RAY DIFFRACTION100
4.55-5.720.17133690.15577070X-RAY DIFFRACTION100
5.72-24.130.20383680.20267238X-RAY DIFFRACTION100

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