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- PDB-7k5f: 1.90 A resolution structure of WT BfrB from Pseudomonas aeruginos... -

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Basic information

Entry
Database: PDB / ID: 7k5f
Title1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor KM-5-50
ComponentsFerroxidase
KeywordsOXIDOREDUCTASE / BIOFILMS / ELECTRON TRANSPORT / IRON STORAGE / IRON BINDING / IRON MOBILIZATION / PROTEIN-PROTEIN INTERACTION INHIBITOR
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / 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 / : / Chem-VXP / Bacterioferritin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLovell, S. / Battaile, K.P. / Soldano, A. / Punchi-Hewage, A. / Meraz, K. / Annor-Gyamfi, J.K. / Yao, H. / Bunce, R.A. / Rivera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125529 United States
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Small Molecule Inhibitors of the Bacterioferritin (BfrB)-Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas aeruginosa Cells.
Authors: Soldano, A. / Yao, H. / Punchi Hewage, A.N.D. / Meraz, K. / Annor-Gyamfi, J.K. / Bunce, R.A. / Battaile, K.P. / Lovell, S. / Rivera, M.
History
DepositionSep 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)229,21128
Polymers222,96212
Non-polymers6,24916
Water17,889993
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)458,42256
Polymers445,92424
Non-polymers12,49832
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)129.582, 194.445, 203.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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

#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 (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: bfrB, PA3531 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY79, ferroxidase
#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 / Heme B


Mass: 616.487 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-VXP / 4-{[(3-chloro-5-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione


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


Mass: 18.015 Da / Num. of mol.: 993 / 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: 2.87 Å3/Da / Density % sol: 57.17 % / Mosaicity: 0.11 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 30% (v/v) PEG 200, 0.1M sodium acetate, 0.1M NaCl

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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 PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.61 Å / Num. obs: 183439 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.2 / Num. measured all: 1261509 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.95-1.987.11.0376366189480.767298.1
10.68-48.616.60.03814212270.99948.598.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.17rc2_3615refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D8O

5d8o


Resolution: 1.95→48.61 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 9186 5.01 %
Rwork0.1783 174183 -
obs0.1804 183369 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.91 Å2 / Biso mean: 34.3426 Å2 / Biso min: 16.54 Å2
Refinement stepCycle: final / Resolution: 1.95→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15195 0 414 993 16602
Biso mean--41.47 41.81 -
Num. residues----1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116087
X-RAY DIFFRACTIONf_angle_d0.9421852
X-RAY DIFFRACTIONf_dihedral_angle_d18.6319528
X-RAY DIFFRACTIONf_chiral_restr0.0462355
X-RAY DIFFRACTIONf_plane_restr0.0062800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.970.32113030.2725708601198
1.97-20.30713100.26155711602198
2-2.020.2943150.24615689600498
2.02-2.050.28552880.23775728601698
2.05-2.070.2673080.2225693600198
2.07-2.10.27663000.22445724602498
2.1-2.130.28293270.21445769609698
2.13-2.160.26733110.20995705601698
2.16-2.20.25972740.19845787606199
2.2-2.230.25132960.19255757605398
2.23-2.270.27432990.19765748604799
2.27-2.310.24352860.18645772605899
2.31-2.360.22783140.18185745605999
2.36-2.40.25492920.18915787607999
2.4-2.460.24822950.17435762605799
2.46-2.510.20622910.16825812610399
2.51-2.580.21383150.16765797611299
2.58-2.650.21572920.17055829612199
2.65-2.720.21223240.18045775609999
2.72-2.810.22763160.18025820613699
2.81-2.910.23513130.1745791610499
2.91-3.030.22943060.19185828613499
3.03-3.170.24943110.19965884619599
3.17-3.330.23532850.19155878616399
3.33-3.540.21363300.1858496179100
3.54-3.820.20693210.167158706191100
3.82-4.20.17133230.144358886211100
4.2-4.810.15673210.126359256246100
4.81-6.060.20782970.167960096306100
6.06-48.610.20533230.18256143646699

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