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- PDB-7k5g: 1.95 A resolution structure of WT BfrB from Pseudomonas aeruginos... -

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Basic information

Entry
Database: PDB / ID: 7k5g
Title1.95 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor KM-5-28
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 / : / Chem-VXS / Bacterioferritin BfrB
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)230,65433
Polymers222,96212
Non-polymers7,69221
Water14,772820
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)461,30966
Polymers445,92424
Non-polymers15,38442
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
MethodPISA
Unit cell
Length a, b, c (Å)129.739, 194.791, 202.343
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


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


Mass: 296.321 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C17H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 57.1 % / Mosaicity: 0.09 °
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: Mar 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.7 Å / Num. obs: 185188 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Net I/σ(I): 13.5 / Num. measured all: 1248238 / Scaling rejects: 210
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.95-1.9871.0476360291390.7612.2100
10.68-48.76.50.033792612220.99945.498.3

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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→46.75 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 9218 4.98 %
Rwork0.1576 175792 -
obs0.1593 185010 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.47 Å2 / Biso mean: 27.4335 Å2 / Biso min: 9.16 Å2
Refinement stepCycle: final / Resolution: 1.95→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15003 0 545 820 16368
Biso mean--37 36.13 -
Num. residues----1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115979
X-RAY DIFFRACTIONf_angle_d0.90521708
X-RAY DIFFRACTIONf_dihedral_angle_d17.3959431
X-RAY DIFFRACTIONf_chiral_restr0.0462344
X-RAY DIFFRACTIONf_plane_restr0.0052743
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 (%)
1.95-1.970.28943100.238757916101100
1.97-20.2462870.210658706157100
2-2.020.26662970.194558296126100
2.02-2.050.22273190.189757816100100
2.05-2.070.23793010.194257996100100
2.07-2.10.21662910.181458396130100
2.1-2.130.21053110.16458356146100
2.13-2.160.18292810.150858976178100
2.16-2.20.19793110.1557616072100
2.2-2.230.19173270.149558066133100
2.23-2.270.28253090.22815764607399
2.27-2.310.18673210.141758066127100
2.31-2.360.20593160.143858296145100
2.36-2.40.18473020.140558556157100
2.4-2.460.17133160.133558326148100
2.46-2.510.1962990.136158426141100
2.51-2.580.17633230.133258116134100
2.58-2.650.20282980.136558796177100
2.65-2.720.18833210.144558496170100
2.72-2.810.19082820.142958796161100
2.81-2.910.19453060.141458506156100
2.91-3.030.18253160.159258626178100
3.03-3.170.19183030.163459026205100
3.17-3.330.19923250.166158606185100
3.33-3.540.17312950.165759026197100
3.54-3.820.18413210.155258966217100
3.82-4.20.16283010.13958986199100
4.2-4.810.16542820.129959686250100
4.81-6.050.18623300.173759626292100
6.06-46.750.20763170.18416138645599

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