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- PDB-7k5h: 1.90 A resolution structure of WT BfrB from Pseudomonas aeruginos... -

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Basic information

Entry
Database: PDB / ID: 7k5h
Title1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor KM-5-66
ComponentsFerroxidase
KeywordsOXIDOREDUCTASE / BIOFILMS / ELECTRON TRANSPORT / IRON STORAGE / IRON BINDING / IRON MOBILIZATION / PROTEIN-PROTEIN INTERACTION INHIBITOR
Function / homology
Function and homology information


ferritin complex / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / 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-VXV / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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)231,03333
Polymers222,96212
Non-polymers8,07121
Water18,2851015
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)462,06666
Polymers445,92424
Non-polymers16,14242
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)129.500, 194.495, 202.952
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-VXV / 4-{[3-(3-chloro-5-hydroxyphenyl)propyl]amino}-1H-isoindole-1,3(2H)-dione


Mass: 330.766 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C17H15ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1015 / 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: 57.08 % / Mosaicity: 0.06 °
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 EIGER2 X 9M / Detector: PIXEL / Date: Aug 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.62 Å / Num. obs: 200059 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.5 / Num. measured all: 1378627 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.9-1.9370.9986934198560.7812.299.9
10.41-48.626.40.047849113370.99729.198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIXdev_3959refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D8O

5d8o


Resolution: 1.9→46.78 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 10031 5.02 %
Rwork0.1578 189925 -
obs0.1594 199956 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.34 Å2 / Biso mean: 28.1415 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 1.9→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15159 0 497 1015 16671
Biso mean--39.58 39.88 -
Num. residues----1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916038
X-RAY DIFFRACTIONf_angle_d0.87921769
X-RAY DIFFRACTIONf_dihedral_angle_d15.2715896
X-RAY DIFFRACTIONf_chiral_restr0.0442343
X-RAY DIFFRACTIONf_plane_restr0.0082764
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 (%)
1.9-1.920.27523640.225262656629100
1.92-1.940.2573430.219662816624100
1.94-1.970.22533220.194762826604100
1.97-1.990.21483550.181262656620100
1.99-2.020.21193380.172162896627100
2.02-2.050.23153300.168462876617100
2.05-2.080.20673430.166662726615100
2.08-2.110.21063220.1662756597100
2.11-2.140.17683310.152362836614100
2.14-2.170.19043130.148263146627100
2.17-2.210.17373240.148663466670100
2.21-2.250.18493400.143662946634100
2.25-2.30.18393240.139363056629100
2.3-2.340.18513190.136563176636100
2.34-2.390.18653350.137863016636100
2.39-2.450.17523210.134463176638100
2.45-2.510.17163260.135462966622100
2.51-2.580.17853710.135162996670100
2.58-2.650.16893220.13863656687100
2.65-2.740.17913340.140862886622100
2.74-2.840.18143740.146462966670100
2.84-2.950.18343290.143963246653100
2.95-3.090.19653060.157164146720100
3.09-3.250.18883290.170263456674100
3.25-3.450.20153040.163963676671100
3.45-3.720.19143400.156763806720100
3.72-4.090.18443360.150363646700100
4.09-4.680.14783490.134164256774100
4.68-5.90.20063440.179964446788100
5.9-46.780.21523430.20626625696899

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