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

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Basic information

Entry
Database: PDB / ID: 9nhr
TitleCrystal structure of structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor KM-5-25
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: 1.95 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

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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)231,67339
Polymers222,96212
Non-polymers8,71127
Water12,520695
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)463,34678
Polymers445,92424
Non-polymers17,42254
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area98610 Å2
ΔGint-581 kcal/mol
Surface area121670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.569, 194.357, 203.032
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
11D-202-

HEM

21D-202-

HEM

31D-202-

HEM

41L-201-

HEM

51L-201-

HEM

61L-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 , 5 types, 722 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-A1BYB / 4-{[(5-chloro-2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione


Mass: 302.712 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H11ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.87 Å3/Da / Density % sol: 57.09 %
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: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 3, 2021
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.59 Å / Num. obs: 185210 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 1.04 / Net I/σ(I): 12.5 / Num. measured all: 1284414
Reflection shellResolution: 1.95→1.98 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 1.043 / Num. measured all: 61051 / Num. unique obs: 9123 / CC1/2: 0.746 / Rpim(I) all: 0.435 / Rrim(I) all: 1.131 / Χ2: 1.03 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(dev_4210: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→38 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 9277 5.01 %
Rwork0.1798 --
obs0.1819 185107 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15173 0 590 695 16458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116194
X-RAY DIFFRACTIONf_angle_d0.92621954
X-RAY DIFFRACTIONf_dihedral_angle_d15.4365978
X-RAY DIFFRACTIONf_chiral_restr0.0462348
X-RAY DIFFRACTIONf_plane_restr0.0082780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.30393140.26745807X-RAY DIFFRACTION100
1.97-20.29552910.25295830X-RAY DIFFRACTION100
2-2.020.30473230.24565820X-RAY DIFFRACTION100
2.02-2.050.26583270.22965758X-RAY DIFFRACTION100
2.05-2.070.25152850.21875817X-RAY DIFFRACTION100
2.07-2.10.24843060.21145816X-RAY DIFFRACTION100
2.1-2.130.27923230.20685855X-RAY DIFFRACTION100
2.13-2.160.25532990.20885852X-RAY DIFFRACTION100
2.16-2.20.26043070.19385784X-RAY DIFFRACTION100
2.2-2.230.22652980.18435852X-RAY DIFFRACTION100
2.23-2.270.23183300.18475811X-RAY DIFFRACTION100
2.27-2.310.22872940.17785825X-RAY DIFFRACTION100
2.31-2.360.2432970.18215849X-RAY DIFFRACTION100
2.36-2.40.24753100.18135834X-RAY DIFFRACTION100
2.4-2.460.22032980.17575843X-RAY DIFFRACTION100
2.46-2.510.21292870.1725843X-RAY DIFFRACTION100
2.51-2.580.21713580.16965814X-RAY DIFFRACTION100
2.58-2.650.21082880.16695882X-RAY DIFFRACTION100
2.65-2.720.23193220.17955845X-RAY DIFFRACTION100
2.72-2.810.23432970.17055845X-RAY DIFFRACTION100
2.81-2.910.20453090.16235848X-RAY DIFFRACTION100
2.91-3.030.21662660.17585892X-RAY DIFFRACTION100
3.03-3.170.23563350.18595885X-RAY DIFFRACTION100
3.17-3.330.2343040.18715887X-RAY DIFFRACTION100
3.33-3.540.20933020.17325885X-RAY DIFFRACTION100
3.54-3.820.20073280.17315878X-RAY DIFFRACTION100
3.82-4.20.20163150.15645904X-RAY DIFFRACTION100
4.2-4.810.16623160.14485941X-RAY DIFFRACTION100
4.81-6.050.2353250.19095975X-RAY DIFFRACTION100
6.05-380.21893230.19636153X-RAY DIFFRACTION100

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